Nucleic acid molecules from rice encoding proteins for abiotic stress tolerance, enhanced yeild, disease resistance and altered nutritional quality and uses thereof

ABSTRACT

The present invention encompasses nucleic acid molecules isolated from Oryza sativa that encode proteins for conferring abiotic stress tolerance, enhanced yield, disease resistance, or altered nutritional composition in plants. The invention further relates to expression of these molecules in microorganisms and transgenic plants for altering these characteristics of the organism.

[0001] This application claims the benefit of U.S. Provisional Application No. 60/334,501 filed Nov. 30, 2001, which is incorporated by reference herein in its entirety.

FIELD OF THE INVENTION

[0002] The present invention pertains to nucleic acid molecules isolated from Oryza sativa comprising nucleotide sequences that encode proteins for abiotic stress tolerance, enhanced yield, disease resistance or altered nutritional quality. The invention particularly relates to methods of using nucleic acid molecules and/or proteins from Rice in transgenic plants to conferthe above-identified agronomic traits.

BACKGROUND OF THE INVENTION

[0003] Improvement of the agronomic characteristics of crop plants has been ongoing since the beginning of agriculture. Most of the land suitable for crop production is currently being used. As human populations continue to increase, improved crop varieties will be required to adequately provide our food and feed (Trewavas (2001) Plant Physiol. 125: 174-179). To avoid catastrophic famines and malnutrition, future crop cultivars will need to have improved yields with equivalent farm inputs. These cultivars will need to more effectively withstand adverse conditions such as drought, soil salinity or disease, which will be especially important as marginal lands are brought into cultivation. Finally, we will need cultivars with altered nutrient composition to enhance human and animal nutrition, and to enable more efficient food and feed processing, by designing cultivars for specific end-uses.

[0004] Recent scientific advances have together identified many candidate genes associated with traits of agronomic interest. Scientific approaches used to identify genes involved in a pathway or response of interest associated with an agronomic trait include genetics, genomics, bioinformatics, and functional genomics. Genetics is the scientific study of the mechanisms of inheritance. By identifying mutations which alter the pathway or response of interest, classical (or forward) genetics can help to identify the genes involved in these pathways or responses. For example, a mutant with enhanced susceptibility to disease may identify an important component of the plant signal transduction pathway leading from pathogen recognition to disease resistance. Genomics is the system-level study of an organism's genome, including genes and corresponding gene products—RNA and proteins. Genomic approaches have provided sequence information from diverse plant species, including full-length and partial cDNA sequences; more recently the complete genomic sequence of Arabidopsis thaliana became available. A unique proprietary resource used for purposes of this invention is the Syngenta draft genomic sequence of rice (Oryza sativa). As part of genomics, bioinformatics approaches process raw sequence information and can be used, for example, to help identify genes in a genomic sequence.

[0005] Functional genomics is the assignment of function to genes and their products. Functional genomics makes use of a variety of approaches to identify genes in a particular pathway or response of interest. The use of genetics to help assign function is described in the paragraph above. Using, for example, similarity searches, alignments and phylogenetic analyses, bioinformatics can often identify homologs of a gene product of interest. Very similar homologs (eg. >˜90% amino acid identity over the entire length of the protein) are very likely orthologs, i.e. share the same function in different organisms. Thus bioinformatics is another approach to assigning function to genes identified through genomics.

[0006] Functional genomics can make use of additional approaches. Expression analysis uses high density DNA microarrays to monitor the mRNA expression of thousands of genes in a single experiment. Experimental treatments can include those eliciting a response of interest, such as the disease resistance response in plants infected with a pathogen. To give additional examples of the use of microarrays, mRNA expression levels can be monitored in distinct tissues over a developmental time course, or in mutants affected in a response of interest. Proteomics can also help to assign function, by assaying the expression and post-translational modifications of hundreds of proteins in a single experiment. Proteomics approaches are in many cases analogous to the approaches taken for monitoring mRNA expression in microarray experiments. Protein-protein interactions can also help to assign proteins to a given pathway or response, by identifying proteins which interact with known components of the pathway or response. For functional genomics, protein-protein interactions are often studied using large-scale yeast two-hybrid assays. Another approach to assigning gene function is to express the corresponding protein in a heterologous host, for example the bacterium Escherichia coli, followed by purification and enzymatic assays.

[0007] The generation and analysis of plants transgenic for a gene of interest can be used for plant functional genomics, with several advantages. The gene can often be both overexpressed and underexpressed (“knocked out”), thereby increasing the chances of observing a phenotype linking the gene to a pathway or response of interest. Two aspects of transgenic functional genomics help lend a high level of confidence to functional assignment by this approach. First, phenotypic observations are carried out in the context of the living plant. Second, the range of phenotypes observed often correlates well with observed expression levels.

[0008] Transgenic functional genomics is especially valuable in improved cultivar development. Only genes that function in a pathway or response of interest, and that in addition are able to confer a desired trait-based phenotype, are promoted to candidate genes for crop improvement efforts. Such efforts can take various forms, for example the generation of transgenic crops or marker-assisted breeding using desirable alleles of the gene.

SUMMARY OF THE INVENTION

[0009] This Summary of Invention lists several embodiments of the invention, and in many cases lists variations and permutations of these embodiments. This Summary is merely exemplary of the numerous and varied embodiments. Mention of one or more preferred features of a given embodiment is likewise exemplary. Such embodiment can typically exist with or without the feature(s) mentioned; likewise, those features can be applied to other embodiments of the invention, whether listed in this Summary or not. To avoid excessive repetition, this Summary does not list or suggest all possible combinations of such features.

[0010] Embodiments of the present invention provide nucleotide and amino acid sequences known as cDNAs from rice.

[0011] Embodiments of the present invention relate to an isolated nucleic acid comprising or consisting of a nucleotide sequence including:

[0012] (a) a nucleotide sequence listed in odd numbered sequences of SEQ ID NO:1-63, fragment, domain, or feature thereof;

[0013] (b) a nucleotide sequence having substantial similarity to (a);

[0014] (c) a nucleotide sequence capable of hybridizing to (a);

[0015] (d) a nucleotide sequence complementary to (a), (b) or (c); and

[0016] (e) a nucleotide sequence which is the reverse complement of (a), (b) or (c).

[0017] In a preferred embodiment, the substantial similarity is at least about 65% identity, preferably about 80% identity, preferably 90%, and more preferably at least about 95% identity to the nucleotide sequence listed in odd numbered sequences of SEQ ID Nos:1-63, fragment, domain, or feature thereof.

[0018] In a preferred embodiment, the sequence having substantial similarity to the nucleotide sequence listed in odd numbered sequences of SEQ ID Nos:1-63, fragment, domain, or feature thereof, is from a plant. In a preferred embodiment, the plant is a dicot. In another preferred embodiment, the plant is a gymnosperm. In a more preferred embodiment, the plant is a monocot. In another preferred embodiment, the plant is rice, wheat, barley, rye, corn, potato, canola, soybean, sunflower, carrot, sweet potato, sugarbeet, bean, pea, chicory, lettuce, cabbage, cauliflower, broccoli, turnip, radish, spinach, asparagus, onion, garlic, eggplant, pepper, celery, squash, pumpkin, cucumber, apple, pear, quince, melon, plum, cherry, peach, nectarine, apricot, strawberry, grape, raspberry, blackberry, pineapple, avocado, papaya, mango, banana, soybean, tobacco, tomato, sorghum or sugarcane. In a more preferred embodiment, the monocot is a cereal. In a more preferred embodiment, the cereal may be, for example, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum sp., or teosinte. In a most preferred embodiment, the cereal is rice.

[0019] In a preferred embodiment, the nucleic acid is expressed in a specific location or tissue of a plant. In a more preferred embodiment, the location or tissue is for example, but not limited to, epidermis, vascular tissue, meristem, cambium, cortex, pith, leaf, and flower. In a most preferred embodiment, the location or tissue is a leaf, sheath, flower, root or seed. In another preferred embodiment, the nucleic acid encodes a polypeptide involved in a function such as, for example, but not limited to, carbon metabolism, photosynthesis, signal transduction, cell growth, reproduction, disease processes, gene regulation, and differentiation. In a more preferred embodiment, the nucleic acid encodes a polypeptide involved in abiotic stress tolerance, enhanced yield, disease resistance, or nutritional content.

[0020] In a preferred embodiment, the isolated nucleic acid comprising or consisting of a nucleotide sequence capable of hybridizing to a nucleotide sequence listed in odd numbered sequences of SEQ ID Nos:1-63, or fragment, domain, or feature thereof. In a preferred embodiment, hybridization allows the sequence to form a duplex atmedium or high stringency. Embodiments of the present invention also encompass a nucleotide sequence complementary to a nucleotide sequence listed in odd numbered sequences of SEQ ID Nos:1-63, or fragment, domain, or feature thereof. Embodiments of the present invention further encompass a nucleotide sequence complementary to a nucleotide sequence that has substantial similarity or is capable of hybridizing to a nucleotide sequence listed in odd numbered sequences of SEQ ID Nos:1-63, or fragment, domain, or feature thereof.

[0021] In a preferred embodiment, the nucleotide sequence having substantial similarity is an allelic variant of the nucleotide sequence listed in odd numbered sequences of SEQ ID Nos:1-63, or fragment, domain, or feature thereof. In an alternate embodiment, the sequence having substantial similarity is a naturally occurring variant. In another alternate embodiment, the sequence having substantial similarity is a polymorphic variant of the nucleotide sequence listed in odd numbered sequences of SEQ ID Nos:1-63, or fragment, domain, or feature thereof.

[0022] In a preferred embodiment, the isolated nucleic acid contains a plurality of regions having the nucleotide sequence listed in odd numbered sequences of SEQ ID Nos:1-63, or exon, domain, or feature thereof.

[0023] In a preferred embodiment, the isolated nucleic acid contains a polypeptide-encoding sequence. In a more preferred embodiment, the polypeptide-encoding sequence contains a 20 base pair nucleotide portion identical in sequence to a consecutive 20 base pair nucleotide portion of a nucleic acid sequence listed in odd numbered sequences of SEQ ID Nos:1-63. In a more preferred embodiment, the polypeptide contains a polypeptide sequence listed in even numbered sequences of SEQ ID Nos:2-64, or a fragment thereof. In a more preferred embodiment, a polypeptide described in Tables 1-4. In a more preferred embodiment, the polypeptide is a plant polypeptide. In a more preferred embodiment, the plant is a dicot. In a more preferred embodiment, the plant is a gymnosperm. In a more preferred embodiment, the plant is a monocot. In a more preferred embodiment, the monocot is a cereal. In a more preferred embodiment, the cereal may be, for example, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, miloflax, gramma grass, Tripsacum, and teosinte. In a most preferred embodiment, the cereal is rice.

[0024] In one embodiment, the polypeptide is expressed throughout the plant. In a more preferred embodiment, the polypeptide is expressed in a specific location or tissue of a plant. In a more preferred embodiment, the location or tissue may be, for example, epidermis, root, vascular tissue, meristem, cambium, cortex, pith, leaf, and flower. In a most preferred embodiment, the location or tissue is a seed.

[0025] In a preferred embodiment, the polypeptide is involved in a function such as abiotic stress tolerance, enhanced yield, disease resistance or nutritional content.

[0026] In a preferred embodiment, the sequence of the isolated nucleic acid encodes a polypeptide useful for generating an antibody having immunoreactivity against a polypeptide encoded by a nucleotide sequence listed in even numbered sequences of SEQ ID Nos:2-64, or fragment, domain, or feature thereof.

[0027] In a preferred embodiment, the sequence having substantial similarity contains a deletion or insertion of at least one nucleotide. In a more preferred embodiment, the deletion or insertion is of less than about thirty nucleotides. In a most preferred embodiment, the deletion or insertion is of less than about five nucleotides.

[0028] In a preferred embodiment, the sequence of the isolated nucleic acid having substantial similarity comprises or consists of a substitution in at least one codon. In a preferred embodiment, the substitution is conservative.

[0029] Embodiments of the present invention also relate to the an isolated nucleic acid molecule comprising or consisting of a nucleotide sequence, its complement, or its reverse complement, encoding a polypeptide including:

[0030] (a) a polypeptide sequence listed in even numbered sequences of SEQ ID Nos:2-64, or a fragment, domain, repeat, feature, or chimera thereof;

[0031] (b) a polypeptide sequence having substantial similarity to (a);

[0032] (c) a polypeptide sequence encoded by a nucleotide sequence identical to or having substantial similarity to a nucleotide sequence listed in odd numbered sequences of SEQ ID Nos:1-63, or a fragment, domain, or feature thereof, or a sequence complementary thereto;

[0033] (d) a polypeptide sequence encoded by a nucleotide sequence capable of hybridizing under medium stringency conditions to a nucleotide sequence listed in odd numbered sequences of SEQ ID Nos:1-63, or to a sequence complementary thereto; and

[0034] (e) a functional fragment of (a), (b), (c) or (d).

[0035] In another preferred embodiment, the polypeptide having substantial similarity is an allelic variant of a polypeptide sequence listed in even numbered sequences of SEQ ID NOS:2-64, or a fragment, domain, repeat, feature, or chimeras thereof. In another preferred embodiment, the isolated nucleic acid includes a plurality of regions from the polypeptide sequence encoded by a nucleotide sequence identical to or having substantial similarity to a nucleotide sequence listed in odd numbered sequences of SEQ ID NOS:1-63, or fragment, domain, or feature thereof, or a sequence complementary thereto.

[0036] In another preferred embodiment, the polypeptide is a polypeptide sequence listed in even numbered sequences of SEQ ID NOS:2-64. In another preferred embodiment, the polypeptide is a functional fragment or domain. In yet another preferred embodiment, the polypeptide is a chimera, where the chimera may include functional protein domains, including domains, repeats, post-translational modification sites, or other features. In a more preferred embodiment, the polypeptide is a plant polypeptide. In a more preferred embodiment, the plant is a dicot. In a more preferred embodiment, the plant is a gymnosperm. In a more preferred embodiment, the plant is a monocot. In a more preferred embodiment, the monocot is a cereal. In a more preferred embodiment, the cereal may be, for example, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum, and teosinte. In a most preferred embodiment, the cereal is rice.

[0037] In a preferred embodiment, the polypeptide is expressed in a specific location or tissue of a plant. In a more preferred embodiment, the location or tissue may be, for example, epidermis, root, vascular tissue, meristem, cambium, cortex, pith, leaf, and flower. In a more preferred embodiment, the location or tissue is a seed.

[0038] In a preferred embodiment, the polypeptide is involved in a function such as abiotic stress tolerance, disease resistance, enhanced yield or nutritional quality or composition.

[0039] In a preferred embodiment, the polypeptide sequence encoded by a nucleotide sequence having substantial similarity to a nucleotide sequence listed in odd numbered sequences of SEQ ID Nos:1-63 or a fragment, domain, or feature thereof or a sequence complementary thereto, includes a deletion or insertion of at least one nucleotide. In a more preferred embodiment, the deletion or insertion is of less than about thirty nucleotides. In a most preferred embodiment, the deletion or insertion is of less than about five nucleotides.

[0040] In a preferred embodiment, the polypeptide sequence encoded by a nucleotide sequence having substantial similarity to a nucleotide sequence listed in odd numbered sequences of SEQ ID Nos:1-63, or fragment, domain, or feature thereof or a sequence complementary-thereto, includes a substitution of at least one codon. In a more preferred embodiment, the substitution is conservative.

[0041] In a preferred embodiment, the polypeptide sequences having substantial similarity to the polypeptide sequence listed in even numbered sequences of SEQ ID Nos:2-64, or a fragment, domain, repeat, feature, or chimeras thereof includes a deletion or insertion of at least one amino acid.

[0042] In a preferred embodiment, the polypeptide sequences having substantial similarity to the polypeptide sequence listed in even numbered sequences of SEQ ID Nos:2-64, or a fragment, domain, repeat, feature, or chimeras thereof includes a substitution of at least one amino acid.

[0043] Embodiments of the present invention also relate to a shuffled nucleic acid containing a plurality of nucleotide sequence fragments, wherein at least one of the fragments corresponds to a region of a nucleotide sequence listed in odd numbered sequences of SEQ ID NOS:1-63, and wherein at least two of the plurality of sequence fragments are in an order, from 5′ to 3′ which is not an order in which the plurality of fragments naturally occur in a nucleic acid. In a more preferred embodiment, all of the fragments in a shuffled nucleic acid containing a plurality of nucleotide sequence fragments are from a single gene. In a more preferred embodiment, the plurality of fragments originates from at least two different genes. In a more preferred embodiment, the shuffled nucleic acid is operably linked to a promoter sequence. Another more preferred embodiment is a chimeric polynucleotide including a promoter sequence operably linked to the shuffled nucleic acid. In a more preferred embodiment, the shuffled nucleic acid is contained within a host cell.

[0044] Embodiments of the present invention also contemplate an expression cassette including a promoter sequence optably linked to an isolated nucleic acid containing a nucleotide sequence including:

[0045] (a) a nucleotide sequence listed in odd numbered sequences of SEQ ID NOS:1-63, or fragment, domain, or feature thereof;

[0046] (b) a nucleotide sequence having substantial similarity to (a);

[0047] (c) a nucleotide sequence capable of hybridizing to (a);

[0048] (d) a nucleotide sequence complementary to (a), (b) or (c); and

[0049] (e) a nucleotide sequence which is the reverse complement of (a), (b) or (c).

[0050] Further encompassed within the invention is a recombinant vector comprising an expression cassette according to embodiments of the present invention. Also encompassed are plant cells, which contain expression cassettes, according to the present disclosure, and plants, containing these plant cells. In a preferred embodiment, the plant is a dicot. In another preferred embodiment, the plant is a gymnosperm. In another preferred embodiment, the plant is a monocot. In a more preferred embodiment, the monocot is a cereal. In a more preferred embodiment, the cereal may be, for example, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum and teosinte. In a most preferred embodiment, the cereal is rice.

[0051] In one embodiment, the expression cassette is expressed throughout the plant. In another embodiment, the expression cassette is expressed in a specific location or tissue of a plant. In a preferred embodiment, the location or tissue may be, for example, epidermis, root, vascular tissue, meristem, cambium, cortex, pith, leaf, and flower. In a more preferred embodiment, the location or tissue is a seed.

[0052] In one embodiment, the expression cassette is involved in a function such as, for example, but not limited to, disease resistance, yield, abiotic stress resistance, nutritional quality, carbon metabolism, photosynthesis, signal transduction, cell growth, reproduction, disease processes, gene regulation, and differentiation. In a more preferred embodiment, the chimeric polypeptide is involved in a function such as, abiotic stress tolerance, enhanced yield, disease resistance or nutritional composition.

[0053] In one embodiment, the plant contains a modification to a phenotype or measurable characteristic of the plant, the modification being attributable to theexpression cassette. In a preferred embodiment, the modification may be, for example, nutritional enhancement, increased nutrient uptake efficiency, enhanced production of endogenous compounds, and production of heterologous compounds. In another preferred embodiment, the modification includes having increased or decreased resistance to an herbicide, a stress, or a pathogen. In another preferred embodiment, the modification includes having enhanced or diminished requirement for light, water, nitrogen, or trace elements. In another preferred embodiment, the modification includes being enriched for an essential amino acid as a proportion of a protein fraction of the plant. In a more preferred embodiment, the protein fraction may be, for example, total seed protein, soluble protein, insoluble protein, water-extractable protein, and lipid-associated protein. In another preferred embodiment, the modification includes overexpression, underexpression, antisense modulation, sense suppression, inducible expression, inducible repression, or inducible modulation of a gene.

[0054] Embodiments of the present invention also provide seed and isolated product from plants which contain an expression cassette including a promoter sequence operably linked to an isolated nucleic acid containing a nucleotide sequence including:

[0055] (a) a nucleotide sequence listed in odd numbered sequences of SEQ ID NOS:1-63, or fragment, domain, or feature thereof;

[0056] (b) a nucleotide sequence encoding a polypeptide of even numbered sequences of SEQ ID NOS:2-64, fragment, domain or feature thereof;

[0057] (c) a nucleotide sequence having substantial similarity to (a) or (b);

[0058] (d) a nucleotide sequence capable of hybridizing to (a), (b) or (c);

[0059] (e) a nucleotide sequence complementary to (a), (b), (c) or (d); and

[0060] (f) a nucleotide sequence that is the reverse complement of (a), (b), (c) or (d) according to the present disclosure.

[0061] In a preferred embodiment the isolated product includes an enzyme, a nutritional protein, a structural protein, an amino acid, a lipid, a fatty acid, a polysaccharide, a sugar, an alcohol, an alkaloid, a carotenoid, a propanoid, a steroid, a pigment, a vitamin and a plant hormone.

[0062] Embodiments of the present invention also relate to isolated products produced by expression of an isolated nucleic acid containing a nucleotide sequence including:

[0063] (a) a nucleotide sequence listed in odd numbered sequences of SEQ ID NOS:1-63, or fragment, domain, or feature thereof;

[0064] (b) a nucleotide sequence encoding a polypeptide listed in even numbered sequences of SEQ ID NOS: 2-64, or fragment, domain or feature thereof;

[0065] (c) a nucleotide sequence having substantial similarity to (a) or (b);

[0066] (d) a nucleotide sequence capable of hybridizing to (a) or (b);

[0067] (e) a nucleotide sequence complementary to (a), (b), (c) or (d); and

[0068] (f) a nucleotide sequence that is the reverse complement of (a), (b) (c) or (d) according to the present disclosure.

[0069] In a preferred embodiment, the product is produced in a plant. In another preferred embodiment, the product is produced in cell culture. In another preferred embodiment, the product is produced in a cell-free system. In another preferred embodiment, the product includes an enzyme, a nutritional protein, a structural protein, an amino acid, a lipid, a fatty acid, a polysaccharide, a sugar, an alcohol, an alkaloid, a carotenoid, a propanoid, a steroid, a pigment, a vitamin and a plant hormone.

[0070] In a preferred embodiment, the product is a polypeptide containing an amino acid sequence listed in even numbered sequences of SEQ ID NOS:2-64. In a more preferred embodiment, the protein is an enzyme.

[0071] Embodiments of the present invention further relate to an isolated polynucleotide including a nucleotide sequence of at least 10 bases, which sequence is identical, complementary, or substantially similar to a region of any sequence of odd numbered sequences of SEQ ID NOS:1-63, and wherein the polynucleotide is adapted for any of numerous uses.

[0072] In a preferred embodiment, the polynucleotide is used as a chromosomal marker. In another preferred embodiment, the polynucleotide is used as a marker for RFLP analysis. In another preferred embodiment, the polynucleotide is used as a marker for quantitative trait linked breeding. In another preferred embodiment, the polynucleotide is used as a marker for marker-assisted breeding. In another preferred embodiment, the polynucleotide is used as a bait sequence in a two-hybrid system to identify sequence-encoding polypeptides interacting with the polypeptide encoded by the bait sequence. In another preferred embodiment, the polynucleotide is used as a diagnostic indicator for genotyping or identifying an individual or population of individuals. In another preferred embodiment, the polynucleotide is used for genetic analysis to identify boundaries of genes or exons.

[0073] Embodiments of the present invention also relate to an expression vector comprising or consisting of a nucleic acid molecule including:

[0074] (a) a nucleic acid encoding a polypeptide as listed in even numbered sequences of SEQ ID NOS:2-64;

[0075] (b) a fragment, one or more domains, or featured regions listed in odd numbered sequences of SEQ ID NOS:1-63; and

[0076] (c) a complete nucleic acid sequence listed in odd numbered sequences of SEQ ID NOS:1-63, or a fragment thereof, in combination with a heterologous sequence.

[0077] In a preferred embodiment, the expression vector includes one or more elements such as, for example, but not limited to, a promoter-enhancer sequence, a selection marker sequence, an origin of replication, an epitope-tag encoding sequence, or an affinity purification-tag encoding sequence. In a more preferred embodiment, the promoter-enhancer sequence may be, for example, the CaMV 35S promoter, the CaMV 19S promoter, the tobacco PR-1a promoter, ubiquitin and the phaseolin promoter. In another embodiment, the promoter is operable in plants, and more preferably, a constitutive or inducible promoter. In another preferred embodiment, the selection marker sequence encodes an antibiotic resistance gene. In another preferred embodiment, the epitope-tag sequence encodes V5, the peptide Phe-His-His-Thr-Thr, hemagglutinin, or glutathione-S-transferase. In another preferred embodiment the affinity purification-tag sequence encodes a polyamino acid sequence or a polypeptide. In a more preferred embodiment, the polyamino acid sequence is polyhistidine. In a more preferred embodiment, the polypeptide is chitin binding domain or glutathione-S-transferase. In a more preferred embodiment, the affinity purification-tag sequence comprises an intein encoding sequence.

[0078] In a preferred embodiment, the expression vector is a eukaryotic expression vector or a prokaryotic expression vector. In a more preferred embodiment, the eukaryotic expression vector includes a tissue-specific promoter. More preferably, the expression vector is operable in plants.

[0079] Embodiments of the present invention also relate to a cell comprising or consisting of a nucleic acid construct comprising an expression vector and a nucleic acid including a nucleic acid encoding a polypeptide as listed in even numbered sequences of SEQ ID NOS:2-64, or a nucleic acid sequence listed in odd numbered sequences of SEQ ID NOS:1-63, or a segment thereof, in combination with a heterologous sequence.

[0080] In a preferred embodiment, the cell is a bacterial cell, a fungal cell, a plant cell, or an animal cell. In a more preferred embodiment, the polypeptide is expressed in a specific location or tissue of a plant. In a most preferred embodiment, the location or tissue may be, for example, epidermis, root, vascular tissue, meristem, cambium, cortex, pith, leaf, and flower. In an alternate most preferred embodiment, the location or tissue is a seed. In a preferred embodiment, the polypeptide is involved in a function such as, for example, carbon metabolism, photosynthesis, signal transduction, cell growth, reproduction, disease processes, gene regulation, and differentiation. More preferably, the polypeptide is involved in a function such as, abiotic stress tolerance, enhanced yield, disease resistance or nutritional composition.

[0081] Embodiments of the present invention also relate to polypeptides encoded by the isolated nucleic acid molecules of the present disclosure including a polypeptide containing a polypeptide sequence encoded by an isolated nucleic acid containing a nucleotide sequence including:

[0082] (a) a nucleotide sequence listed in odd numbered sequences of SEQ ID NOS:1-63, or exon, domain, or feature thereof;

[0083] (b) a nucleotide sequence having substantial similarity to (a);

[0084] (c) a nucleotide sequence capable of hybridizing to (a);

[0085] (d) a nucleotide sequence complementary to (a), (b) or (c); and

[0086] (e) a nucleotide sequence which is the reverse complement of (a), (b) or (c);

[0087] (f) or a functional fragment thereof.

[0088] A polypeptide containing a polypeptide sequence encoded by an isolated nucleic acid containing a nucleotide sequence, its complement, or its reverse complement, encoding a polypeptide including a polypeptide sequence including:

[0089] (a) a polypeptide sequence listed in even numbered sequences of SEQ ID NOS:2-64, or a domain, repeat, feature, or chimeras thereof;

[0090] (b) a polypeptide sequence having substantial similarity to (a);

[0091] (c) a polypeptide sequence encoded by a nucleotide sequence identical to or having substantial similarity to a nucleotide sequence listed in odd numbered sequences of SEQ ID NOS:1-63, or an exon, domain, or feature thereof, or a sequence complementary thereto;

[0092] (d) a polypeptide sequence encoded by a nucleotide sequence capable of hybridizing under medium stringency conditions to a nucleotide sequence listed in odd numbered sequences of SEQ ID NOS:1-63, or to a sequence complementary thereto; and

[0093] (e) a functional fragment of (a), (b), (c) or (d);

[0094] (f) or a functional fragment thereof.

[0095] Embodiments of the present invention contemplate a polypeptide containing a polypeptide sequence encoded by an isolated nucleic acid which includes a shuffled nucleic acid containing a plurality of nucleotide sequence fragments, wherein at least one of the fragments corresponds to a region of a nucleotide sequence listed in odd numbered sequences of SEQ ID NOS:1-63, and wherein at least two of the plurality of sequence fragments are in an order, from 5′ to 3′ which is not an order in which the plurality of fragments naturally occur in a nucleic acid, or functional fragment thereof.

[0096] Embodiments of the present invention contemplate a polypeptide containing a polypeptide sequence encoded by an isolated polynucleotide containing a nucleotide sequence of at least 10 bases, which sequence is identical, complementary, or substantially similar to a region of any of sequences of odd numbered sequences of SEQ ID NOS:1-63, and wherein the polynucleotide is adapted for a use including:

[0097] (a) use as a chromosomal marker to identify the location of the corresponding or complementary polynucleotide on a native or artificial chromosome;

[0098] (b) use as a marker for RFLP analysis;

[0099] (c) use as a marker for quantitative trait linked breeding;

[0100] (d) use as a marker for marker-assisted breeding;

[0101] (e) use as a bait sequence in a two-hybrid system to identify sequence encoding polypeptides interacting with the polypeptide encoded by the bait sequence;

[0102] (f) use as a diagnostic indicator for genotyping or identifying an individual or population of individuals; and

[0103] (g) use for genetic analysis to identify boundaries of genes or exons;

[0104] (h) or functional fragment thereof.

[0105] Embodiments of the present invention also contemplate an isolated polypeptide containing a polypeptide sequence including:

[0106] (a) a polypeptide sequence listed in even numbered sequences of SEQ ID NOS:2-64, or exon, domain, or feature thereof;

[0107] (b) a polypeptide sequence having substantial similarity to (a);

[0108] (c) a polypeptide sequence encoded by a nucleotide sequence identical to or having substantial similarity to a nucleotide sequence listed in odd numbered sequences of SEQ ID NOS:1-63, or an exon, domain, or feature thereof, or a sequence complementary thereto;

[0109] (d) a polypeptide sequence encoded by a nucleotide sequence capable of hybridizing under medium stringency conditions to a nucleotide sequence listed in odd numbered sequences of SEQ ID NOS:1-63, or to a sequence complementary thereto; and

[0110] (e) a functional fragment of (a), (b), (c) or (d).

[0111] In a preferred embodiment, the substantial similarity is at least about 65% identity. In a more preferred embodiment, the substantial similarity is at least about 80% identity. In a most preferred embodiment, the substantial similarity is at least about 95% identity. In a preferred embodiment, the substantial similarity is at least three percent greater than the percent identity to the closest homologous sequence listed in any of the Tables.

[0112] In a preferred embodiment, the sequence having substantial similarity is from a plant. In a more preferred embodiment, the plant is a dicot. In a more preferred embodiment, the plant is a gymnosperm. In a more preferred embodiment, the plant is a monocot. In a more preferred embodiment, the monocot is a cereal. In a more preferred embodiment, the cereal may be, for example, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum and teosinte. In a most preferred embodiment, the cereal is rice.

[0113] In a preferred embodiment, the polypeptide is expressed in a specific location or tissue of a plant. In a more preferred embodiment, the location or tissue may be, for example, epidermis, root, vascular tissue, meristem, cambium, cortex, pith, leaf, and flower. In a more preferred embodiment, the location or tissue is a seed. In a preferred embodiment, the polypeptide is involved in a function such as, for example, carbon metabolism, photosynthesis, signal transduction, cell growth, reproduction, disease processes, gene regulation, and differentiation.

[0114] In a preferred embodiment, hybridization of a polypeptide sequence encoded by a nucleotide sequence identical to or having substantial similarity to a nucleotide sequence listed in odd numbered sequences of SEQ ID NOS:1-63, or an exon, domain, or feature thereof, or a sequence complementary thereto, or a polypeptide sequence encoded by a nucleotide sequence capable of hybridizing under medium stringency conditions to a nucleotide sequence listed in odd numbered sequences of SEQ ID NOS:1-63, or to a sequence complementary thereto, allows the sequence to form a duplex atmedium or high stringency.

[0115] In a preferred embodiment, a polypeptide having substantial similarity to a polypeptide sequence listed in even numbered sequences of SEQ ID NOS:2-64, or exon, domain, or feature thereof, is an allelic variant of the polypeptide sequence listed in even numbered sequences of SEQ ID NOS:2-64. In another preferred embodiment, a polypeptide having substantial similarity to a polypeptide sequence listed in even numbered sequences of SEQ ID NOS:2-64, or exon, domain, or feature thereof, is a naturally occurring variant of the polypeptide sequence listed in even numbered sequences of SEQ ID NOS:2-64. In another preferred embodiment, a polypeptide having substantial similarity to a polypeptide sequence listed in even numbered sequences of SEQ ID NOS:2-64, or exon, domain, or feature thereof, is a polymorphic variant of the polypeptide sequence listed in even numbered sequences of SEQ ID NOS:2-64.

[0116] In an alternate preferred embodiment, the sequence having substantial similarity contains a deletion or insertion of at least one amino acid. In a more preferred embodiment, the deletion or insertion is of less than about ten amino acids. In a most preferred embodiment, the deletion or insertion is of less than about three amino acids.

[0117] In a preferred embodiment, the sequence having substantial similarity encodes a substitution in at least one amino acid.

[0118] Also contemplated is a method of producing a plant comprising a modification thereto, including the steps of: (1) providing a nucleic acid which is an isolated nucleic acid containing a nucleotide sequence including:

[0119] (a) a nucleotide sequence listed in odd numbered sequences of SEQ ID NOS:1-63, or exon, domain, or feature thereof;

[0120] (b) a nucleotide sequence having substantial similarity to (a);

[0121] (c) a nucleotide sequence capable of hybridizing to (a);

[0122] (d) a nucleotide sequence complementary to (a), (b) or (c); and

[0123] (e) a nucleotide sequence which is the reverse complement of (a), (b) or (c); and (2) introducing the nucleic acid into the plant, wherein the nucleic acid is expressible in the plant in an amount effective to effect the modification. In one embodiment, the modification comprises an altered trait in the plant, wherein the trait corresponds to the nucleic acid introduced into the plant. In other preferred embodiments, the altered trait is related to a feature listed in any of Tables 1-4, and it is particularly preferred when the trait corresponds to disease resistance, yield, abiotic stress resistance, nutritional composition, carbon metabolism, photosynthesis, signal transduction, cell growth, reproduction, disease processes, or differentiation.

[0124] In another embodiment, the modification includes an increased or decreased expression or accumulation of a product of the plant. Preferably, the product is a natural product of the plant. Equally preferably, the product is a new or altered product of the plant. Preferably, the product includes, but is not limited to, an enzyme, a nutritional protein, a structural protein, an amino acid, a lipid, a fatty acid, a polysaccharide, a sugar, an alcohol, an alkaloid, a carotenoid, a propanoid, a steroid, a pigment, a vitamin and a plant hormone. Another preferred embodiment provides method of controlling a pathogen by delivering an effective amount of a product resulting from modification of the plant.

[0125] Embodiments of the present invention also include a method of controlling a pathogen sensitive to a product, including expressing an isolated nucleic acid containing a nucleotide sequence including:

[0126] (a) a nucleotide sequence listed odd numbered sequences of SEQ ID Nos:1-63, or exon, domain, or feature thereof;

[0127] (b) a nucleotide sequence having substantial similarity to (a);

[0128] (c) a nucleotide sequence capable of hybridizing to (a);

[0129] (d) a nucleotide sequence complementary to (a), (b) or (c); and

[0130] (e) a nucleotide sequence which is the reverse complement of (a), (b) or (c); thereby causing the plant to produce the product. In preferred embodiments, the product is selected from the group consisting of an enzyme, a nutritional protein, a structural protein, an amino acid, a lipid, a fatty acid, a polysaccharide, a sugar, an alcohol, an alkaloid, a carotenoid, a propanoid, a steroid, a pigment, a vitamin and a plant hormone.

[0131] Also encompassed within the presently disclosed invention is a method of producing a recombinant protein, comprising the steps of:

[0132] (a) growing recombinant cells comprising a nucleic acid construct under suitable growth conditions, the construct comprising an expression vector and a nucleic acid including: a nucleic acid encoding a protein as listed in even numbered nucleotide sequences of SEQ ID NOS:2-64, or a nucleic acid sequence listed in odd numbered nucleotide sequences of SEQ ID NOS:1-63, or segments thereof; and

[0133] (b) isolating from the recombinant cells the recombinant protein expressed thereby.

[0134] Embodiments of the present invention provide a method of producing a recombinant protein in which the expression vector includes one or more elements including a promoter-enhancer sequence, a selection marker sequence, an origin of replication, an epitope-tag encoding sequence, and an affinity purification-tag encoding sequence. In one preferred embodiment, the nucleic acid construct includes an epitope-tag encoding sequence and the isolating step includes use of an antibody specific for the epitope-tag. In another preferred embodiment, the nucleic acid construct contains a polyamino acid encoding sequence and the isolating step includes use of a resin comprising a polyamino acid binding substance, preferably where the polyamino acid is polyhistidine and the polyamino binding resin is nickel-charged agarose resin. In yet another preferred embodiment, the nucleic acid construct contains a polypeptide encoding sequence and the isolating step includes the use of a resin containing a polypeptide binding substance, preferably where the polypeptide is a chitin binding domain and the resin contains chitin-sepharose.

[0135] Embodiments of the present invention also relate to a plant modified by a method that includes introducing into a plant a nucleic acid where the nucleic acid is expressible in the plant in an amount effective to effect the modification. The modification can be, for example, nutritional enhancement, increased nutrient uptake efficiency, enhanced production of endogenous compounds, and production of heterologous compounds. In one embodiment, the modified plant has increased or decreased resistance to an herbicide, a stress, or a pathogen. In another embodiment, the modified plant has enhanced or diminished requirement for light, water, nitrogen, or trace elements. In yet another embodiment, the modified plant is enriched for an essential amino acid as a proportion of a protein fraction of the plant. The protein fraction may be, for example, total seed protein, soluble protein, insoluble protein, water-extractable protein, and lipid-associated protein. The modification may include overexpression, underexpression, antisense modulation, sense suppression, inducible expression, inducible repression, or inducible modulation of a gene.

[0136] The invention further relates to a seed from a modified plant or an isolated product of a modified plant, where the product may be an enzyme, a nutritional protein, a structural protein, an amino acid, a lipid, a fatty acid, a polysaccharide, a sugar, an alcohol, an alkaloid, a carotenoid, a propanoid, a steroid, a pigment, a vitamin and a plant hormone.

[0137] For purposes of summarizing the invention and the advantages achieved over the prior art, certain objects and advantages of the invention have been described above. Of course, it is to be understood that not necessarily all such objects or advantages may be achieved in accordance with any particular embodiment of the invention. Thus, for example, those skilled in the art will recognize that the invention may be embodied or carried out in a manner that achieves or optimizes one advantage or group of advantages as taught herein without necessarily achieving other objects or advantages as may be taught or suggested herein.

[0138] Further aspects, features and advantages of this invention will become apparent from the detailed description of the preferred embodiments that follow.

BRIEF DESCRIPTION OF THE SEQUENCES IN THE SEQUENCE LIST

[0139] Odd numbered SEQ ID NOs:1-63 are nucleotide sequences isolated from Oryza sativa that are more fully described in Tables 1-4 below.

[0140] Even numbered SEQ ID Nos: 2-64 are protein sequences encoded by the immediately preceding nucleotide sequence, e.g., SEQ ID NO:2 is the protein encoded by the nucleotide sequence of SEQ ID NO:1, SEQ ID NO:4 is the protein encoded by the nucleotide sequence of SEQ ID NO:3, etc.

Definitions

[0141] For clarity, certain terms used in the specification are defined and presented as follows:

[0142] “Associated with/operatively linked” refer to two nucleic acid sequences that are related physically or functionally. For example, a promoter or regulatory DNA sequence is said to be “associated with” a DNA sequence that codes for an RNA or a protein if the two sequences are operatively linked, or situated such that the regulator DNA sequence will affect the expression level of the coding or structural DNA sequence.

[0143] A “chimeric construct” is a recombinant nucleic acid sequence in which a promoter or regulatory nucleic acid sequence is operatively linked to, or associated with, a nucleic acid sequence that codes for an mRNA or which is expressed as a protein, such that the regulatory nucleic acid sequence is able to regulate transcription or expression of the associated nucleic acid sequence. The regulatory nucleic acid sequence of the chimeric construct is not normally operatively linked to the associated nucleic acid sequence as found in nature.

[0144] Co-factor: natural reactant, such as an organic molecule or a metal ion, required in an enzyme-catalyzed reaction. A co-factor is e.g. NAD(P), riboflavin (including FAD and FMN), folate, molybdopterin, thiamin, biotin, lipoic acid, pantothenic acid and coenzyme A, S-adenosylmethionine, pyridoxal phosphate, ubiquinone, menaquinone. Optionally, a co-factor can be regenerated and reused.

[0145] A “coding sequence” is a nucleic acid sequence that is transcribed into RNA such as mRNA, rRNA, tRNA, snRNA, sense RNA or antisense RNA. Preferably the RNA is then translated in an organism to produce a protein.

[0146] Complementary: “complementary” refers to two nucleotide sequences that comprise antiparallel nucleotide sequences capable of pairing with one another upon formation of hydrogen bonds between the complementary base residues in the antiparallel nucleotide sequences.

[0147] Enzyme activity: means herein the ability of an enzyme to catalyze the conversion of a substrate into a product. A substrate for the enzyme comprises the natural substrate of the enzyme but also comprises analogues of the natural substrate, which can also be converted, by the enzyme into a product or into an analogue of a product. The activity of the enzyme is measured for example by determining the amount of product in the reaction after a certain period of time, or by determining the amount of substrate remaining in the reaction mixture after a certain period of time. The activity of the enzyme is also measured by determining the amount of an unused co-factor of the reaction remaining in the reaction mixture after a certain period of time or by determining the amount of used co-factor in the reaction mixture after a certain period of time. The activity of the enzyme is also measured by determining the amount of a donor of free energy or energy-rich molecule (e.g. ATP, phosphoenolpyruvate, acetyl phosphate or phosphocreatine) remaining in the reaction mixture after a certain period of time or by determining the amount of a used donor of free energy or energy-rich molecule (e.g. ADP, pyruvate, acetate or creatine) in the reaction mixture after a certain period of time.

[0148] Expression Cassette: “Expression cassette” as used herein means a nucleic acid molecule capable of directing expression of a particular nucleotide sequence in an appropriate host cell, comprising a promoter operatively linked to the nucleotide sequence of interest which is operatively linked to termination signals. It also typically comprises sequences required for proper translation of the nucleotide sequence. The coding region usually codes for a protein of interest but may also code for a functional RNA of interest, for example antisense RNA or a nontranslated RNA, in the sense or antisense direction. The expression cassette comprising the nucleotide sequence of interest may be chimeric, meaning that at least one of its components is heterologous with respect to at least one of its other components. The expression cassette may also be one that is naturally occurring but has been obtained in a recombinant form useful for heterologous expression. Typically, however, the expression cassette is heterologous with respect to the host, i.e., the particular DNA sequence of the expression cassette does not occur naturally in the host cell and must have been introduced into the host cell or an ancestor of the host cell by a transformation event. The expression of the nucleotide sequence in the expression cassette may be under the control of a constitutive promoter or of an inducible promoter that initiates transcription only when the host cell is exposed to some particular external stimulus. In the case of a multicellular organism, such as a plant, the promoter can also be specific to a particular tissue or organ or stage of development.

[0149] Gene: the term “gene” is used broadly to refer to any segment of DNA associated with a biological function. Thus, genes include coding sequences and/or the regulatory sequences required for their expression. Genes also include nonexpressed DNA segments that, for example, form recognition sequences for other proteins. Genes can be obtained from a variety of sources, including cloning from a source of interest or synthesizing from known or predicted sequence information, and may include sequences designed to have desired parameters.

[0150] Heterologous/exogenous: The terms “heterologous” and “exogenous” when used herein to refer to a nucleic acid sequence (e.g. a DNA sequence) or a gene, refer to a sequence that originates from a source foreign to the particular host cell or, if from the same source, is modified from its original form. Thus, a heterologous gene in a host cell includes a gene that is endogenous to the particular host cell but has been modified through, for example, the use of DNA shuffling. The terms also include non-naturally occurring multiple copies of a naturally occurring DNA sequence. Thus, the terms refer to a DNA segment that is foreign or heterologous to the cell, or homologous to the cell but in a position within the host cell nucleic acid in which the element is not ordinarily found. Exogenous DNA segments are expressed to yield exogenous polypeptides.

[0151] A “homologous” nucleic acid (e.g. DNA) sequence is a nucleic acid (e.g. DNA) sequence naturally associated with a host cell into which it is introduced.

[0152] Hybridization: The phrase “hybridizing specifically to” refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent conditions when that sequence is present in a complex mixture (e.g., total cellular) DNA or RNA. “Bind(s) substantially” refers to complementary hybridization between a probe nucleic acid and a target nucleic acid and embraces minor mismatches that can be accommodated by reducing the stringency of the hybridization media to achieve the desired detection of the target nucleic acid sequence.

[0153] Inhibitor: a chemical substance that inactivates the enzymatic activity of a protein such as a biosynthetic enzyme, receptor, signal transduction protein, structural gene product, or transport protein. The term “herbicide”(or “herbicidal compound” is used herein to define an inhibitor applied to a plant at any stage of development, whereby the herbicide inhibits the growth of the plant or kills the plant.

[0154] Interaction: quality or state of mutual action such that the effectiveness or toxicity of one protein or compound on another protein is inhibitory (antagonists) or enhancing (agonists).

[0155] A nucleic acid sequence is “isocoding with” a reference nucleic acid sequence when the nucleic acid sequence encodes a polypeptide having the same amino acid sequence as the polypeptide encoded by the reference nucleic acid sequence.

[0156] Isogenic: plants that are genetically identical, except that they may differ by the presence or absence of a heterologous DNA sequence.

[0157] Isolated: in the context of the present invention, an isolated DNA molecule or an isolated enzyme is a DNA molecule or enzyme that, by the hand of man, exists apart from its native environment and is therefore not a product of nature. An isolated DNA molecule or enzyme may exist in a purified form or may exist in a non-native environment such as, for example, in a transgenic host cell.

[0158] Mature protein: protein from which the transit peptide, signal peptide, and/or propeptide portions have been removed.

[0159] Minimal Promoter the smallest piece of a promoter, such as a TATA element, that can support any transcription. A minimal promoter typically has greatly reduced promoter activity in the absence of upstream activation. In the presence of a suitable transcription factor, the minimal promoter functions to permit transcription.

[0160] Modified Enzyme Activity: enzyme activity different from that which naturally occurs in a plant (i.e. enzyme activity that occurs naturally in the absence of direct or indirect manipulation of such activity by man), which is tolerant to inhibitors that inhibit the naturally occurring enzyme activity.

[0161] Native: refers to a gene that is present in the genome of an untransformed plant cell.

[0162] Naturally occurring: the term “naturally occurring” is used to describe an object that can be found in nature as distinct from being artificially produced by man. For example, a protein or nucleotide sequence present in an organism (including a virus), which can be isolated from a source in nature and which has not been intentionally modified by man in the laboratory, is naturally occurring.

[0163] Nucleic acid: the term “nucleic acid” refers to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form. Unless specifically limited, the term encompasses nucleic acids containing known analogues of natural nucleotides which have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g. degenerate codon substitutions) and complementary sequences and as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al, Nucleic Acid Res. 19: 5081 (1991); Ohtsuka et al., J. Biol. Chem. 260: 2605-2608 (1985); Rossolini et al., Mol. Cell. Probes 8: 91-98 (1994)). The terms “nucleic acid” or “nucleic acid sequence” may also be used interchangeably with gene, cDNA, and mRNA encoded by a gene.

[0164] “ORF” means open reading frame.

[0165] Percent identity: the phrases “percent identical” or “percent identical,” in the context of two nucleic acid or protein sequences, refers to two or more sequences or subsequences that have for example 60%, preferably 70%, more preferably 80%, still more preferably 90%, even more preferably 95%, and most preferably at least 99% nucleotide or amino acid residue identity, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms or by visual inspection. Preferably, the percent identity exists over a region of the sequences that is at least about 50 residues in length, more preferably over a region of at least about 100 residues, and most preferably the percent identity exists over at least about 150 residues. In an especially preferred embodiment, the percent identity exists over the entire length of the coding regions.

[0166] For sequence comparison, typically one sequence acts as a reference sequence to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.

[0167] Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2: 482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48: 443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by visual inspection (see generally, Ausubel et al., infra).

[0168] One example of an algorithm that is suitable for determining percent sequence identity and sequence similarity is the BLAST algorithm, which is described in Altschul et al., J. Mol. Biol. 215: 403-410 (1990). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., 1990). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when the cumulative alignment score falls off by the quantity X from its maximum achieved value, the cumulative score goes to zero or below due to the accumulation of one or more negative-scoring residue alignments, or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89: 10915 (1989)).

[0169] In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA 90: 5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a test nucleic acid sequence is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid sequence to the reference nucleic acid sequence is less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.

[0170] Pre-protein: protein that is normally targeted to a cellular organelle, such as a chloroplast, and still comprises its native transit peptide.

[0171] Purified: the term “purified,” when applied to a nucleic acid or protein, denotes that the nucleic acid or protein is essentially free of other cellular components with which it is associated in the natural state. It is preferably in a homogeneous state although it can be in either a dry or aqueous solution. Purity and homogeneity are typically determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography. A protein that is the predominant species present in a preparation is substantially purified. The term “purified” denotes that a nucleic acid or protein gives rise to essentially one band in an electrophoretic gel. Particularly, it means that the nucleic acid or protein is at least about 50% pure, more preferably at least about 85% pure, and most preferably at least about 99% pure.

[0172] Two nucleic acids are “recombined” when sequences from each of the two nucleic acids are combined in a progeny nucleic acid. Two sequences are “directly” recombined when both of the nucleic acids are substrates for recombination. Two sequences are “indirectly recombined” when the sequences are recombined using an intermediate such as a cross-over oligonucleotide. For indirect recombination, no more than one of the sequences is an actual substrate for recombination, and in some cases, neither sequence is a substrate for recombination.

[0173] “Regulatory elements” refer to sequences involved in controlling the expression of a nucleotide sequence. Regulatory elements comprise a promoter operatively linked to the nucleotide sequence of interest and termination signals. They also typically encompass sequences required for proper translation of the nucleotide sequence.

[0174] Significant Increase: an increase in enzymatic activity that is larger than the margin of error inherent in the measurement technique, preferably an increase by about 2-fold or greater of the activity of the wild-type enzyme in the presence of the inhibitor, more preferably an increase by about 5-fold or greater, and most preferably an increase by about 10-fold or greater.

[0175] Significantly less: means that the amount of a product of an enzymatic reaction is reduced by more than the margin of error inherent in the measurement technique, preferably a decrease by about 2-fold or greater of the activity of the wild-type enzyme in the absence of the inhibitor, more preferably an decrease by about 5-fold or greater, and most preferably an decrease by about 10-fold or greater.

[0176] Specific Binding/Immunological Cross-Reactivity: An indication that two nucleic acid sequences or proteins are substantially identical is that the protein encoded by the first nucleic acid is immunologically cross reactive with, or specifically binds to, the protein encoded by the second nucleic acid. Thus, a protein is typically substantially identical to a second protein, for example, where the two proteins differ only by conservative substitutions. The phrase “specifically (or selectively) binds to an antibody,” or “specifically (or selectively) immunoreactive with,” when referring to a protein or peptide, refers to a binding reaction which is determinative of the presence of the protein in the presence of a heterogeneous population of proteins and other biologics. Thus, under designated immunoassay conditions, the specified antibodies bind to a particular protein and do not bind in a significant amount to other proteins present in the sample. Specific binding to an antibody under such conditions may require an antibody that is selected for its specificity for a particular protein. For example, antibodies raised to the protein with the amino acid sequence encoded by any of the nucleic acid sequences of the invention can be selected to obtain antibodies specifically immunoreactive with that protein and not with other proteins except for polymorphic variants. A variety of immunoassay formats may be used to select antibodies specifically immunoreactive with a particular protein. For example, solid-phase ELISA immunoassays, Western blots, or immunohistochemistry are routinely used to select monoclonal antibodies specifically immunoreactive with a protein. See Harlow and Lane (1988) Antibodies, A Laboratory Manual, Cold Spring Harbor Publications, New York “Harlow and Lane”), for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity. Typically a specific or selective reaction will be at least twice background signal or noise and more typically more than 10 to 100 times background.

[0177] “Stringent hybridization conditions” and “stringent hybridization wash conditions” in the context of nucleic acid hybridization experiments such as Southern and Northern hybridizations are sequence dependent, and are different under different environmental parameters. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology-Hybridization with Nucleic Acid Probes part I chapter 2 “Overview of principles of hybridization and the strategy of nucleic acid probe assays” Elsevier, New York. Generally, highly stringent hybridization and wash conditions are selected to be about 5° C. lower than the thermal melting point (T_(m)) for the specific sequence at a defined ionic strength and pH. Typically, under “stringent conditions” a probe will hybridize to its target subsequence, but to no other sequences.

[0178] The T_(m) is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Very stringent conditions are selected to be equal to the T_(m) for a particular probe. An example of stringent hybridization conditions for hybridization of complementary nucleic acids which have more than 100 complementary residues on a filter in a Southern or northern blot is 50% fonmamide with 1 mg of heparin at 42° C., with the hybridization being carried out overnight. An example of highly stringent wash conditions is 0.1 5M NaCl at 72° C. for about 15 minutes. An example of stringent wash conditions is a 0.2×SSC wash at 65° C. for 15 minutes (see, Sambrook, infra, for a description of SSC buffer). Often, a high stringency wash is preceded by a low stringency wash to remove background probe signal. An example medium stringency wash for a duplex of, e.g., more than 100 nucleotides, is 1×SSC at 45° C. for 15 minutes. An example low stringency wash for a duplex of, e.g., more than 100 nucleotides, is 4-6×SSC at 40° C. for 15 minutes. For short probes (e.g., about 10 to 50 nucleotides), stringent conditions typically involve salt concentrations of less than about 1.0 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3, and the temperature is typically at least about 30° C. Stringent conditions can also be achieved with the addition of destabilizing agents such as formamide. In general, a signal to noise ratio of 2× (or higher) than that observed for an unrelated probe in the particular hybridization assay indicates detection of a specific hybridization. Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the proteins that they encode are substantially identical. This occurs, e.g., when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code.

[0179] The following are examples of sets of hybridization/wash conditions that may be used to clone nucleotide sequences that are homologues of reference nucleotide sequences of the present invention: a reference nucleotide sequence preferably hybridizes to the reference nucleotide sequence in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. with washing in 2×SSC, 0.1% SDS at 50° C., more desirably in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. with washing in 1×SSC, 0.1% SDS at 50° C., more desirably still in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. with washing in 0.5×SSC, 0.1% SDS at 50° C., preferably in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. with washing in 0.1×SSC, 0.1% SDS at 50° C., more preferably in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. with washing in 0.1×SSC, 0.1% SDS at 65° C.

[0180] A “subsequence” refers to a sequence of nucleic acids or amino acids that comprise a part of a longer sequence of nucleic acids or amino acids (e.g., protein) respectively.

[0181] Substrate: a substrate is the molecule that an enzyme naturally recognizes and converts to a product in the biochemical pathway in which the enzyme naturally carries out its function, or is a modified version of the molecule, which is also recognized by the enzyme and is converted by the enzyme to a product in an enzymatic reaction similar to the naturally-occurring reaction.

[0182] Transformation: a process for introducing heterologous DNA into a plant cell, plant tissue, or plant. Transformed plant cells, plant tissue, or plants are understood to encompass not only the end product of a transformation process, but also transgenic progeny thereof.

[0183] “Transformed,” “transgenic,” and “recombinant” refer to a host organism such as a bacterium or a plant into which a heterologous nucleic acid molecule has been introduced. The nucleic acid molecule can be stably integrated into the genome of the host or the nucleic acid molecule can also be present as an extrachromosomal molecule. Such an extrachromosomal molecule can be auto-replicating. Transformed cells, tissues, or plants are understood to encompass not only the end product of a transformation process, but also transgenic progeny thereof. A “non-transformed,” “non-transgenic,” or “non-recombinant” host refers to a wild-type organism, e.g., a bacterium or plant, which does not contain the heterologous nucleic acid molecule.

[0184] Viability: “viability” as used herein refers to a fitness parameter of a plant. Plants are assayed for their homozygous performance of plant development, indicating which proteins are essential for plant growth.

DETAILED DESCRIPTION OF THE INVENTION I. General Description of Trait Functional Genomics Project

[0185] The goal of functional genomics is to assign functions to the genes of an organism using a variety of methodologies, including but not limited to bioinformatics, gene expression studies, gene and gene product interactions, genetics, biochemistry and molecular genetics. For example, bioinformatics can assign function to a given gene by identifying genes in heterologous organisms with a high degree of similarity (homology) at the amino acid or nucleotide level. Expression of a gene at the mRNA or protein levels can assign function by linking expression of a gene to an environmental response, a developmental process or a genetic (mutational) or molecular genetic (gene overexpression or underexpression) perturbation. Expression of a gene at the mRNA level can be ascertained either alone (Northern analysis) or in concert with other genes (microarray analysis), whereas expression of a gene at the protein level can be ascertained either alone (native or denatured protein gel or immunoblot analysis) or in concert with other genes (proteomic analysis). Knowledge of protein/protein and protein/DNA interactions can assign function by identifying proteins and nucleic acid sequences acting together in the same biological process. Genetics can assign function to a gene by demonstrating that DNA lesions (mutations) in the gene have a quantifiable effect on the organism, including but not limited to: its development; hormone biosynthesis and response; growth and growth habit (plant architecture); mRNA expression profiles; protein expression profiles; ability to resist diseases; tolerance of abiotic stresses; ability to acquire nutrients; photosynthetic efficiency; altered primary and secondary metabolism; and the composition of various plant organs. Biochemistry can assign function by demonstrating that the protein encoded by the gene, typically when expressed in a heterologous organism, possesses a certain enzymatic activity, alone or in combination with other proteins. Molecular genetics can assign function by overexpressing or underexpressing the gene in the native plant or in heterologous organisms, and observing quantifiable effects as described in functional assignment by genetics above.

[0186] It is recognized by those skilled in the art that these different methodologies can each provide data as evidence for the function of a particular gene, and that such evidence is stronger with increasing amounts of data used for functional assignment: preferably from a single methodology, more preferably from two methodologies, and even more preferably from more than two methodologies. In addition, those skilled in the art are aware that different methodologies can differ in the strength of the evidence for the assignment of gene function. Typically, but not always, a datum of biochemical, genetic and molecular genetic evidence is considered stronger than a datum of bioinformatic or gene expression evidence. Finally, those skilled in the art recognize that, for different genes, a single datum from a single methodology can differ in terms of the strength of the evidence provided by each distinct datum for the assignment of the function of these different genes.

[0187] The objective of trait functional genomics is to identify crop trait genes, i.e. genes capable of conferring useful agronomic traits in crop plants. Such agronomic traits include, but are not limited to: enhanced yield, whether in quantity or quality; enhanced nutrient acquisition and enhanced metabolic efficiency; enhanced or altered nutrient composition of plant tissues used for food, feed, fiber or processing; enhanced resistance to plant diseases; enhanced tolerance of adverse environmental conditions (abiotic stresses) including but not limited to drought, excessive cold, excessive heat, or excessive soil salinity or extreme acidity or alkalinity; and alterations in plant architecture or development, including changes in developmental timing. The deployment of such identified trait genes could materially improve crop plants for the benefit of agriculture, potentially, irrespective of the method of deployment of such genes.

[0188] Cereals are the most important crop plants on the planet, in terms of both human and animal consumption. Genomic synteny (conservation of gene order within large chromosomal segments) is observed in the rice, maize, wheat, barley, rye, oats and other agriculturally important monocots, which facilitates the mapping and isolation of orthologous genes from diverse cereal species based on the sequence of a single cereal gene. Rice has the smallest (˜420 Mb) genome among the cereal grains, and has recently been a major focus of public and private genomic and EST sequencing efforts.

[0189] To identify crop trait genes in the rice genome, genes with likely or demonstrated effects on agronomic traits of interest as defined above were identified in the scientific literature. The predicted peptides encoded by these genes were then used to search a proprietary database of rice genomic sequences for those with high similarity, using search algorithms familiar to those skilled in the art, resulting in the identification of rice trait gene orthologs. Rice trait gene orthologs were assigned function based on similarity searches of two different public databases: the SwissProt protein database and the GenPept non-redundant (nr) database of conceptual translations of all of the nucleotide sequences in Genbank.

[0190] To demonstrate the validity of this approach, and to provide additional evidence for the function of a subset of these genes, full-length and partial cDNAs of rice trait gene orthologs were isolated. Several different commercially available gene prediction programs were used to help predict full-length cDNAs corresponding to the putative rice trait gene orthologs. Full-length and partial cDNAs were isolated based on these predictions, using two different approaches. In one approach, a similarity search algorithm was used to search a database of sequenced cDNA clones. In another approach, the predicted cDNAs were used in combination with the genomic sequence to design primers for PCR amplification using a commercially available PCR primer-picking program. Primers were use d for PCR amplification of full-length or partial cDNAs from rice cDNA libraries or first-strand cDNA. cDNA clones resulting from either approach were used for the construction of vectors designed for overexpression or underexpression of corresponding genes in transgenic rice plants. Assays to identify transgenic plants for alterations in traits of interest are to be used to unambiguously assign the utility of these genes for the improvement of rice, and by extension, other cereals, either by transgenic or classical breeding methods.

II. Identifying, Cloning and Sequencing cDNAs

[0191] The identification of genes of interest and determination of cDNA homologies is set forth in Example 1. The cloning and sequencing of the cDNAs of the present invention are described in Example 2.

[0192] The isolated nucleic acids and proteins of the present invention are usable over a range of plants, monocots and dicots, in particular monocots such as rice, wheat, barley and maize. In a more preferred embodiment, the monocot is a cereal. In a more preferred embodiment, the cereal may be, for example, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum sp., or teosinte. In a most preferred embodiment, the cereal is rice. Other plants genera include, but are not limited to, Cucurbita, Rosa, Vitis, Juglans, Gragaria, Lotus, Medicago, Onobrychis; Trigonella, Vigna, Citrus, Linum, Geranium, Manihot, Daucus, Arabidopsis, Brassica, Raphanus, Sinapis, Atropa, Capsicum, Datura, Hyoscyamus, Lycopersicon, Nicotiana, Solanum, Petunia, Digitalis, Majorana, Ciahorium, Helianthus, Lactuca, Bromus, Asparagus, Antirrhinum, Heterocallis, Nemesis, Pelargonium, Panieum, Pennisetum, Ranunculus, Senecio, Salpiglossis, Cucumis, Browaalia, Glycine, Pisum, Phaseolus, Lolium, Oryza, Avena, Hordeum, Secale, Allium, and Triticum.

[0193] The present invention also provides a method of genotyping a plant or plant part comprising a nucleic acid molecule of the present invention. Optionally, the plant is a monocot such as, but not limited rice or wheat. Genotyping provides a means of distinguishing homologs of a chromosome pari and can be used to differentiate segregants in a plant population. Molecular marker methods can be used in phylogenetic studies, characterizing genetic relationships among crop varieties, identifying crosses or somatic hybrids, localizing chromosomeal segments affecting mongenic traits, map based cloning, and the study of quantitative inheritance (see Plant Molecular Biology: A Laboratory Manual, Chapter 7, Clark ed., Springer-Verlag, Berlin 1997; Paterson, A. H., “The DNA Revolution”, chapter 2 in Genome Mapping in Plants, Paterson, A. H. ed., Academic Press/R. G. Lands Co., Austin, Tex. 1996).

[0194] The method of genotyping may employ any number of molecular marker analytical techniques such as, but not limited to, restriction length polymorphisms (RFLPs). As is well known in the art, RFLPs are produced by differences in the DNA restriction fragment lengths resulting from nucleotide differences between alleles of the same gene. Thus, the present invention provides a method of following segregation of a gene or nucleic acid of the present invention or chromosomal sequences genetically linked by using RFLP analysis. Linked chromosomal sequences are within 50 centiMorgans (50 cM), within 40 or 30 cM, preferably within 20 or 10 cM, more preferably within 5, 3, 2, or 1 cM of the nucleic acid of the invention.

III. Traits of Interest

[0195] The present invention encompasses the identification and isolation of cDNAs encoding genes of interest in the trait areas of abiotic stress tolerance, enhanced yield, disease resistance, and nutritional composition. Abiotic stresses such as, but not limited to, cold, heat, drought or salt stress can significantly affect the growth and/or yield of plants. Additionally, altering the expression of genes related to these traits are used to improve or modify the rice plants and/or grain as desired. Examples 3-7 describe the isolated genes of interest and methods of analyzing the alteration of expression and their effects on the plant characteristics.

[0196] One aspect of the present invention provides compositions and methods for altering (i.e. increasing or decreasing) the level of nucleic acid molecules and polypeptides of the present invention in plants. In particular, the nucleic acid molecules and polypeptides of the invention are expressed constitutively, temporally or spatially, e.g. at developmental stages, in certain tissues, and/or quantities, which are uncharacteristic of non-recombinantly engineered plants. Therefore, the present invention provides utility in such exemplary applications as altering the specified characteristics identified above.

[0197] Pathogens of the invention include, but are not limited to, fungi, bacteria, nematodes, viruses or viroids, etc.

[0198] Generally Viruses include tobacco or cucumber mosaic virus, ringspot virus, necrosis virus, maize dwarf mosaic virus, etc. Specific fungal, bacterial and viral pathogens of major crops include, but are not limited to: RICE: rice brown spot fungus (Cochliobolus miyabeanus), rice blast fungus—Magnaporthe grisea (Pyricularia grisea), Magnaporthe salvinii (Sclerotium oryzae), Xanthomomas oryzae pv. oryzae, Xanthomomas oryzae pv. oryzicola, Rhizoctonia spp. (including but not limited to Rhizoctonia solani, Rhizoctonia oryzae and Rhizoctonia oryzae-sativae), Pseudomonas spp. (including but not limited to Pseudomonas plantarii, Pseudomonas avenae, Pseudomonas glumae, Pseudomonas fuscovaginae, Pseudomonas alboprecipitans, Pseudomonas syringae pv. panici, Pseudomonas syringae pv. syringae, Pseudomonas syringae pv. oryzae and Pseudomonas syringae pv. aptata), Erwinia spp. (including but not limited to Erwinia herbicola, Erwinia amylovaora, Erwinia chrysanthemi and Erwinia carotovora), Achyla spp. (including but not limited to Achyla conspicua and Achyia klebsiana), Pythium spp. (including but not limited to Pythium dissotocum, Pythium irregulare, Pythium arrhenomanes, Pythium myriotylum, Pythium catenulatum, Pythium graminicola and Pythium spinosum), Saprolegnia spp., Dictyuchus spp., Pythiogeton spp., Phytophthora spp., Alternaria padwickii, Cochliobolus miyabeanus, Curvularia spp. (including but not limited to Curvularia lunata, Curvularia affinis, Curvularia clavata, Curvularia eragrostidis, Curvularia fallax, Curvularia geniculata, Curvularia inaequalis, Curvularia intermedia, Curvularia oryzae, Curvularia oryzae-sativae, Curvularia pallescens, Curvularia senegalensis, Curvularia tuberculata, Curvularia uncinata and Curvularia verruculosa), Sarocladium oryzae, Gerlachia oryzae, Fusarium spp. (including but not limited Fusarium graminearum, Fusarium nivale and to different pathovars of Fusarium monoliforme, including pvs. fujikuroi and zeae), Sclerotium rolfsii, Phoma exigua, Mucor fragilis, Trichoderma viride, Rhizopus spp., Cercospora oryzae, Entyloma oryzae, Dreschlera gigantean, Scierophthora macrospora, Mycovellosiella oryzae, Phomopsis oryzae-sativae, Puccinia graminis, Uromyces coronatus, Cylindrocladium scoparium, Sarocladium oryzae, Gaeumannomyces graminis pv. graminis, Myrothecium verrucaria, Pyrenochaeta oryzae, Ustilaginoidea virens, Neovossia spp. (including but not limited to Neovossia horrida), Tilletia spp., Balansia oryzae-sativae, Phoma spp. (including but not limited to Phoma sorghina, Phoma insidiosa, Phoma glumarum, Phoma glumicola and Phoma oryzina), Nigrospora spp. (including but not limited to Nigrospora oryzae, Nigrospora sphaerica, Nigrospora panici and Nigrospora padwickii), Epiococcum nigrum, Phyllostica spp., Wolkia decolorans, Monascus purpureus, Aspergillus spp., Penicillium spp., Absidia spp., Mucor spp., Chaetomium spp., Dematium spp., Monilia spp., Streptomyces spp., Syncephalastrum spp., Verticillium spp., Nematospora coryli, Nakataea sigmoidea, Cladosporium spp., Bipolaris spp., Coniothyrium spp., Diplodia oryzae, Exserophilum rostratum, Helococera oryzae, Melanomma glumarum, Metashaeria spp., Mycosphaerella spp., Oidium spp., Pestalotia spp., Phaeoseptoria spp., Sphaeropsis spp., Trematosphaerella spp., rice black-streaked dwarf virus, rice dwarf virus, rice gall dwarf virus, barley yellow dwarf virus, rice grassy stunt virus, rice hoja blanca virus, rice necrosis mosaic virus, rice ragged stunt virus, rice stripe virus, rice stripe necrosis virus, rice transitory yellowing virus, rice tungro bacilliform virus, rice tungro spherical virus, rice yellow mottle virus, rice tarsonemid mite virus, Echinochloa hoja blanca virus, Echinochloa ragged stunt virus, orange leaf mycoplasma-like organism, yellow dwarf mycoplasma-like organism, Aphelenchoides besseyi, Ditylenchus angustus, Hirschmanniella spp., Criconemella spp., Meloidogyne spp., Heterodera spp., Pratylenchus spp., Hoplolaimus indicus:

[0199] SOYBEANS: Phytophthora sojae, Fusarium solani f. sp. Glycines, Macrophomina phaseolina, Fusarium, Pythium, Rhizoctonia, Phialophora gregata, Sclerotinia sclerotiorum, Diaporthe phaseolorum var. sojae, Colletotrichum truncatum, Phomopsis longicolla, Cercospora kikuchii, Diaporthe phaseolonum var. meridionalis (and var. caulivora), Phakopsora pachyrhyzi, Fusarium solani, Microsphaera diffusa, Septoria glycines, Cercospora kikuchii, Macrophomina phaseolina, Sclerotinia sclerotiorum, Corynespora cassiicola, Rhizoctonia solani, Cercospora sojina,Phytophthora megasperma fsp. glycinea, Macrophomina phaseolina, Fusarium oxysporum, Diapothe phaseolorum var. sojae (Phomopsis sojae), Diaporthe phaseolorum var. caulivora, Sclerotium rolfsii, Cercospora kikuchii, Cercospora sojina, Peronospora manshurica, Colletotrichum dematium (Colletotichum truncatum), Corynespora cassiicola, Phyllosticta sojicola, Alternaria alternata, Pseudomonas syringae p.v. glycinea, Xanthomonas campestris p.v. phaseoli, Microspaera diffusa, Fusarium semitectum, Phialophora gregata, Soybean mosaic virus, Glomerella glycines, Tobacco Ring spot virus, Tobacco Streak virus, Phakopsora pachyrhizi, Pythium aphanidermatum, Pythium ultimum, Pythium dearyanum, Tomato spotted wilted virus, Heterodera glycines, Fusarium solani, Soybean cyst and root knot nematodes.

[0200] CORN: Fusarium moniliforme var. subglutinans, Erwinia stewartii, Fusarium moniliforme, Gibberella zeae (Fusarium Graminearum), Stenocarpella maydi (Diplodia maydis), Pythium irregulare, Pythium debaryanum, Pythium graminicola, Pythium splendens, Pythium ultimum, Pythium aphanidermatum, Aspergillus flavus, Bipolaris maydis O, T (cochliobolus heterostrophus), Helminthosporium carbonum I, II, and III (Cochliobolus carbonum), Exserohilum turcicum I, II and III, Helminthosporium pedicellatum, Physoderma maydis, Phyllosticta maydis, Kabatie-maydis, Cercospora sorghi, Ustilago maydis, Puccinia sorghi, Puccinia polysora, Macrophomina phaseolina, Penicillium oxalicum, Nigrospora oryzae, Cladosporium herbarum, Curvularia lunata, Curvularia inaequalis, Curvularia pallescens, Clavibacter michiganese subsp. Nebraskense, Trichoderma viride, Maize dwarf Mosaic Virus A and B, Wheat Streak Mosaic Virus, Maize Chlorotic Dwarf Virus, Claviceps sorghi, Pseudonomas avenae, Erwinia chrysantemi p.v. Zea, Erwinia corotovora, Cornstun spiroplasma, Diplodia macrospora, Sclerophthora macrospora, Peronosclerospora sorghi, Peronoscherospora philippinesis, Peronosclerospora maydis, Peronosclerospora sacchari, Spacelotheca reiliana, Physopella zea, Cephalosporium maydis, Caphalosporium acremonium, Maize Chlorotic Mottle Virus, High Plains Virus, Maize Mosaic Virus, Maize Rayado Fino Virus, Maize Streak Virus, Maize Stripe Virus, Maize Rought Dwarf Virus:

[0201] WHEAT: Pseudomonas syringae p.v. atrofaciens, Urocystis agropyri, Xanthomonas campestris p.v. translucens, Pseudomonas syringae p.v. syringae, Alternaria alternata, Cladosporium herbarum, Fusarium graminearum, Fusarium avenaceum, Fusarium culmorum, Ustilago tritici, Ascochyta tritici, Cephalosporium gramineum, Collotetrichum graminicola, Erysiphe graminis f. sp. Tritici, Puccinia graminis f. sp. Tritici, Puccinia recondite f. sp. tritici, puccinia striiformis, Pyrenophora triticirepentis, Septoria nodorum, Septoria tritici, Spetoria avenae, Pseudocercosporella herpotrichoides, Rhizoctonia solani, Rhizoctonia cerealis, Gaeumannomyces graminis var. tritici, Pythium aphanidermatum, Pythium arrhenomanes, Pythium ultimum, Bipolaris sorokiniana, Barley Yellow Dwarf Virus, Brome Mosaic Virus, Soil Borne Wheat Mosaic Virus, Wheat Streak Virus, Wheat Spindle Streak Virus, American Wheat Striate Virus, Claviceps purpurea, Tilletia tritici, Tilletia laevis, Pstilago tritici, Tilletia indica, Rhizoctonia solani, Pythium arrhenomannes, Pythium gramicola, Pythium aphanidermatum, High Plains Virus, European Wheat Striate Virus:

[0202] CANOLA: Albugo candida, Alternaria brassicae, Leptosharia maculans, Rhizoctonia solani, Sclerotinia sclerotiorum, Mycospaerella brassiccola, Pythium ultimum, Peronospora parasitica, Fusarium roseum, Alternaria alternata:

[0203] SUNFLOWER: Plasmophora halstedii, Scherotinia sclerotiorum, Aster Yellows, Septoria helianthi, Phomopsis helianthi, Alternaria helianthi, Alternaria zinniae, Botrytis cinera, Phoma macdonaldii, Macrophomina phaseolina, Erysiphe cichoracearum, Phizopus oryzae, Rhizopus arrhizus, Rhizopus stolonifer, Puccinia helianthi, Verticillium Dahliae, Erwinia carotovorum p.v. carotovora, Cephalosporium acremonium, Phytophthora cryptogea, Albugo tragopogonis: etc.

[0204] SORGHUM: Exserohilum turcicum, Colletotrichum graminicola (Glomerella graminicola), Cercospora sorghi, Gloeocercospora sorghi, Ascochyta sorghi, Pseudomonas syringae p.v. syringae, Xanthomonas campestris p.v. holcicola, Pseudomonas andropogonis, Puccinia purpurea, Macrophomina phaseolina, Periconia circinata, Fusarium moniliforme, Alternaria alternate, Bipolaris sorghicola, Helminthosporium sorghicola, Curvularia lunata, Phoma insidiosa, Pseudomonas avenae (Pseudomonas alboprecipitans), Ramulispora sorghi, Ramulispora sorghicola, Phyllachara sacchari Sporisorium relianum (Sphacelotheca reliana), Sphacelotheca cruenta, Sporisorium sorghi, Sugarcane mosaic H, Maize Dwarf Mosaic Virus A & B, Claviceps sorghi, Rhizoctonia solani, Acremonium strictum, Sclerophthona macrospora, Peronosclerospora sorghi, Peronosclerospora philippinensis, Sclerospora graminicola, Fusarium graminearum, Fusarium Oxysporum, Pythium arrhenomanes, Pythium graminicola, etc.

[0205] ALFALFA: Clavibater michiganensis subsp. Insidiosum, Pythium ultimum, Pythium irregulare, Pythium splendens, Pythium debaryanum, Pythium aphanidermatum, Phytophthora megasperma, Peronospora trifoliorum, Phoma medicaginis var. medicaginis, Cercospora medicaginis, Pseudopeziza medicaginis, Leptotrochila medicaginis, Fusarium oxysporum, Rhizoctonia solani, Uromyces striatus, Colletotrichum trifolii race 1 and race 2, Leptosphaerulina briosiana, Stemphylium botryosum, Stagonospora meliloti, Sclerotinia trifoliorum, Alfalfa Mosaic Virus, Verticillium albo-atrum, Xanthomonas campestris p.v. alfalfae, Aphanomyces euteiches, Stemphylium herbarum, Stemphylium alfalfae.

VI. Controlling Gene Expression in Transgenic Plants

[0206] The invention further relates to transformed cells comprising the nucleic acid molecules, transformed plants, seeds, and plant parts, and methods of modifying phenotypic traits of interest by altering the expression of the genes of the invention.

A. Modification of Coding Sequences and Adjacent Sequences

[0207] The transgenic expression in plants of genes derived from heterologous sources may involve the modification of those genes to achieve and optimize their expression in plants. In particular, bacterial ORFs which encode separate enzymes but which are encoded by the same transcript in the native microbe are best expressed in plants on separate transcripts. To achieve this, each microbial ORF is isolated individually and cloned within a cassette which provides a plant promoter sequence at the 5′ end of the ORF and a plant transcriptional terminator at the 3′ end of the ORF. The isolated ORF sequence preferably includes the initiating ATG codon and the terminating STOP codon but may include additional sequence beyond the initiating ATG and the STOP codon. In addition, the ORF may be truncated, but still retain the required activity; for particularly long ORFs, truncated versions which retain activity may be preferable for expression in transgenic organisms. By “plant promoter” and “plant transcriptional terminator” it is intended to mean promoters and transcriptional terminators which operate within plant cells. This includes promoters and transcription terminators which may be derived from non-plant sources such as viruses (an example is the Cauliflower Mosaic Virus).

[0208] In some cases, modification to the ORF coding sequences and adjacent sequence is not required. It is sufficient to isolate a fragment containing the ORF of interest and to insert it downstream of a plant promoter. For example, Gaffney et al. (Science 261: 754-756 (1993)) have expressed the Pseudomonas nahG gene in transgenic plants under the control of the CaMV 35S promoter and the CaMV tml terminator successfully without modification of the coding sequence and with nucleotides of the Pseudomonas gene upstream of the ATG still attached, and nucleotides downstream of the STOP codon still attached to the nahG ORF. Preferably as little adjacent microbial sequence should be left attached upstream of the ATG and downstream of the STOP codon. In practice, such construction may depend on the availability of restriction sites.

[0209] In other cases, the expression of genes derived from microbial sources may provide problems in expression. These problems have been well characterized in the art and are particularly common with genes derived from certain sources such as Bacillus. These problems may apply to the nucleotide sequence of this invention and the modification of these genes can be undertaken using techniques now well known in the art. The following problems may be encountered:

[0210] 1. Codon Usage.

[0211] The preferred codon usage in plants differs from the preferred codon usage in certain microorganisms. Comparison of the usage of codons within a cloned microbial ORF to usage in plant genes (and in particular genes from the target plant) will enable an identification of the codons within the ORF which should preferably be changed. Typically plant evolution has tended towards a strong preference of the nucleotides C and G in the third base position of monocotyledons, whereas dicotyledons often use the nucleotides A or T at this position. By modifying a gene to incorporate preferred codon usage for a particular target transgenic species, many of the problems described below for GC/AT content and illegitimate splicing will be overcome.

[0212] 2. GC/AT Content.

[0213] Plant genes typically have a GC content of more than 35%. ORF sequences which are rich in A and T nucleotides can cause several problems in plants. Firstly, motifs of ATTTA are believed to cause destabilization of messages and are found at the 3′ end of many short-lived mRNAs. Secondly, the occurrence of polyadenylation signals such as AATAAA at inappropriate positions within the message is believed to cause premature truncation of transcription. In addition, monocotyledons may recognize AT-rich sequences as splice sites (see below).

[0214] 3. Sequences Adjacent to the Initiating Methionine.

[0215] Plants differ from microorganisms in that their messages do not possess a defined ribosome binding site. Rather, it is believed that ribosomes attach to the 5′ end of the message and scan for the first available ATG at which to start translation. Nevertheless, it is believed that there is a preference for certain nucleotides adjacent to the ATG and that expression of microbial genes can be enhanced by the inclusion of a eukaryotic consensus translation initiator at the ATG. Clontech (1993/1994 catalog, page 210, incorporated herein by reference) have suggested one sequence as a consensus translation initiator for the expression of the E. coli uidA gene in plants. Further, Joshi (N.A.R. 15: 6643-6653 (1987), incorporated herein by reference) has compared many plant sequences adjacent to the ATG and suggests another consensus sequence. In situations where difficulties are encountered in the expression of microbial ORFs in plants, inclusion of one of these sequences at the initiating ATG may improve translation. In such cases the last three nucleotides of the consensus may not be appropriate for inclusion in the modified sequence due to their modification of the second AA residue. Preferred sequences adjacent to the initiating methionine may differ between different plant species. A survey of 14 maize genes located in the GenBank database provided the following results: Position Before the Initiating ATG in 14 Maize Genes: −10 −9 −8 −7 −6 −5 −4 −3 −2 −1 C 3 8 4 6 2 5 6 0 10  7 T 3 0 3 4 3 2 1 1 1 0 A 2 3 1 4 3 2 3 7 2 3 G 6 3 6 0 6 5 4 6 1 5

[0216] This analysis can be done for the desired plant species into which the nucleotide sequence is being incorporated, and the sequence adjacent to the ATG modified to incorporate the preferred nucleotides.

[0217] 4. Removal of Illegitimate Splice Sites.

[0218] Genes cloned from non-plant sources and not optimized for expression in plants may also contain motifs which may be recognized in plants as 5′ or 3′ splice sites, and be cleaved, thus generating truncated or deleted messages. These sites can be removed using the techniques well known in the art.

[0219] Techniques for the modification of coding sequences and adjacent sequences are well known in the art. In cases where the initial expression of a microbial ORF is low and it is deemed appropriate to make alterations to the sequence as described above, then the construction of synthetic genes can be accomplished according to methods well known in the art. These are, for example, described in the published patent disclosures EP 0 385 962 (to Monsanto), EP 0 359 472 (to Lubrizol) and WO 93/07278 (to Ciba-Geigy), all of which are incorporated herein by reference. In most cases it is preferable to assay the expression of gene constructions using transient assay protocols (which are well known in the art) prior to their transfer to transgenic plants.

B. Construction of Plant Expression Cassettes

[0220] Coding sequences intended for expression in transgenic plants are first assembled in expression cassettes behind a suitable promoter expressible in plants. The expression cassettes may also comprise any further sequences required or selected for the expression of the transgene. Such sequences include, but are not restricted to, transcription terminators, extraneous sequences to enhance expression such as introns, vital sequences, and sequences intended for the targeting of the gene product to specific organelles and cell compartments. These expression cassettes can then be easily transferred to the plant transformation vectors described below. The following is a description of various components of typical expression cassettes.

[0221] 1. Promoters

[0222] The selection of the promoter used in expression cassettes will determine the spatial and temporal expression pattern of the transgene in the transgenic plant. Selected promoters will express transgenes in specific cell types (such as leaf epidermal cells, mesophyll cells, root cortex cells) or in specific tissues or organs (roots, leaves or flowers, for example) and the selection will reflect the desired location of accumulation of the gene product. Alternatively, the selected promoter may drive expression of the gene under various inducing conditions. Promoters vary in their strength, i.e., ability to promote transcription. Depending upon the host cell system utilized, any one of a number of suitable promoters can be used, including the gene's native promoter. The following are non-limiting examples of promoters that may be used in expression cassettes.

[0223] a. Constitutive Expression, the Ubiquitin Promoter:

[0224] Ubiquitin is a gene product known to accumulate in many cell types and its promoter has been cloned from several species for use in transgenic plants (e.g. sunflower—Binet et al. Plant Science 79: 87-94 (1991); maize—Christensen et al. Plant Molec. Biol. 12: 619-632 (1989); and Arabidopsis—Callis et al., J. Biol. Chem. 265: 12486-12493 (1990) and Norris et al., Plant Mol. Biol. 21: 895-906 (1993)). The maize ubiquitin promoter has been developed in transgenic monocot systems and its sequence and vectors constructed for monocot transformation are disclosed in the patent publication EP 0 342 926 (to Lubrizol) which is herein incorporated by reference. Taylor et al. (Plant Cell Rep. 12: 491495 (1993)) describe a vector (pAHC25) that comprises the maize ubiquitin promoter and first intron and its high activity in cell suspensions of numerous monocotyledons when introduced via microprojectile bombardment. The Arabidopsis ubiquitin promoter is ideal for use with the nucleotide sequences of the present invention. The ubiquitin promoter is suitable for gene expression in transgenic plants, both monocotyledons and dicotyledons. Suitable vectors are derivatives of pAHC25 or any of the transformation vectors described in this application, modified by the introduction of the appropriate ubiquitin promoter and/or intron sequences.

[0225] b. Constitutive Expression, the CaMV 35S Promoter:

[0226] Construction of the plasmid pCGN1761 is described in the published patent application EP 0 392 225 (Example 23), which is hereby incorporated by reference. pCGN1761 contains the “double” CaMV 35S promoter and the tml transcriptional terminator with a unique EcoRI site between the promoter and the terminator and has a pUC-type backbone. A derivative of pCGN1761 is constructed which has a modified polylinker which includes Notl and XhoI sites in addition to the existing EcoRI site. This derivative is designated pCGN1761ENX. pCGN1761ENX is useful for the cloning of cDNA sequences or coding sequences (including microbial ORF sequences) within its polylinker for the purpose of their expression under the control of the 35S promoter in transgenic plants. The entire 35S promoter-coding sequence-tml terminator cassette of such a construction can be excised by HindIII, SphI, SalI, and Xbal sites 5′ to the promoter and Xbal, BamHI and BglI sites 3′) to the terminator for transfer to transformation vectors such as those described below. Furthermore, the double 35S promoter fragment can be removed by 5′ excision with HindIII, SphI, SalI, Xbal, or Pstl, and 3′ excision with any of the polylinker restriction sites (EcoRI, Notl or XhoI) for replacement with another promoter. If desired, modifications around the cloning sites can be made by the introduction of sequences that may enhance translation. This is particularly useful when overexpression is desired. For example, pCGN1761ENX may be modified by optimization of the translational initiation site as described in Example 37 of U.S. Pat. No. 5,639,949, incorporated herein by reference.

[0227] c. Constitutive Expression, the Actin Promoter:

[0228] Several isoforms of actin are known to be expressed in most cell types and consequently the actin promoter is a good choice for a constitutive promoter. In particular, the promoter from the rice Actl gene has been cloned and characterized (McElroy et al. Plant Cell 2: 163-171 (1990)). A 1.3 kb fragment of the promoter was found to contain all the regulatory elements required for expression in rice protoplasts. Furthermore, numerous expression vectors based on the Actl promoter have been constructed specifically for use in monocotyledons (McElroy et al. Mol. Gen. Genet. 231: 150-160 (1991)). These incorporate the Actl-intron 1, Adhl 5′ flanking sequence and Adhl-intron 1 (from the maize alcohol dehydrogenase gene) and sequence from the CaMV 35S promoter. Vectors showing highest expression were fusions of 35S and Actl intron or the Actl 5′ flanking sequence and the Actl intron. Optimization of sequences around the initiating ATG (of the GUS reporter gene) also enhanced expression. The promoter expression cassettes described by McElroy et al. (Mol. Gen. Genet. 231: 150-160 (1991)) can be easily modified for gene expression and are particularly suitable for use in monocotyledonous hosts. For example, promoter-containing fragments is removed from the McElroy constructions and used to replace the double 35S promoter in pCGN1761ENX, which is then available for the insertion of specific gene sequences. The fusion genes thus constructed can then be transferred to appropriate transformation vectors. In a separate report, the rice Actl promoter with its first intron has also been found to direct high expression in cultured barley cells (Chibbar et al. Plant Cell Rep. 12: 506-509 (1993)).

[0229] d. Inducible Expression, PR-1 Promoters:

[0230] The double 35S promoter in pCGN1761 ENX may be replaced with any other promoter of choice that will result in suitably high expression levels. By way of example, one of the chemically regulatable promoters described in U.S. Pat. No. 5,614,395, such as the tobacco PR-1 promoter, may replace the double 35S promoter. Alternately, the Arabidopsis PR-1 promoter described in Lebel et al., Plant J. 16: 223-233 (1998) may be used. The promoter of choice is preferably excised from its source by restriction enzymes, but can alternatively be PCR-amplified using primers that carry appropriate terminal restriction sites. Should PCR-amplification be undertaken, then the promoter should be re-sequenced to check for amplification errors after the cloning of the amplified promoter in the target vector. The chemically/pathogen regulatable tobacco PR-1a promoter is cleaved from plasmid pCIB1004 (for construction, see example 21 of EP 0332 104, which is hereby incorporated by reference) and transferred to plasmid pCGN1761ENX (Uknes et al., Plant Cell 4: 645-656 (1992)). pCIB1004 is cleaved with Ncol and the resultant 3′ overhang of the linearized fragment is rendered blunt by treatment with T4 DNA polymerase. The fragment is then cleaved with HindIII and the resultant PR-1a promoter-containing fragment is gel purified and cloned into pCGN1761ENX from which the double 35S promoter has been removed. This is done by cleavage with XhoI and blunting with T4 polymerase, followed by cleavage with HindIII and isolation of the larger vector-terminator containing fragment into which the pCIB1004 promoter fragment is cloned. This generates a pCGN1761ENX derivative with the PR-1a promoter and the tml terminator and an intervening polylinker with unique EcoRI and Notl sites. The selected coding sequence can be inserted into this vector, and the fusion products (i.e. promoter-gene-terminator) can subsequently be transferred to any selected transformation vector, including those described infra. Various chemical regulators may be employed to induce expression of the selected coding sequence in the plants transformed according to the present invention, including the benzothiadiazole, isonicotinic acid, and salicylic acid compounds disclosed in U.S. Pat. Nos. 5,523,311 and 5,614,395.

[0231] e. Inducible Expression, an Ethanol-Inducible Promoter:

[0232] A promoter inducible by certain alcohols or ketones, such as ethanol, may also be used to confer inducible expression of a coding sequence of the present invention. Such a promoter is for example the alcA gene promoter from Aspergillus nidulans (Caddick et al. (1998) Nat. Biotechnol 16:177-180). In A. nidulans, the alcA gene encodes alcohol dehydrogenase 1, the expression of which is regulated by the AlcR transcription factors in presence of the chemical inducer. For the purposes of the present invention, the CAT coding sequences in plasmid palcA:CAT comprising a alcA gene promoter sequence fused to a minimal 35S promoter (Caddick et al. (1998) Nat. Biotechnol 16:177-180) are replaced by a coding sequence of the present invention to form an expression cassette having the coding sequence under the control of the alcA gene promoter. This is carried out using methods well known in the art.

[0233] f. Inducible Expression, a Glucocorticoid-lnducible Promoter:

[0234] Induction of expression of a nucleic acid sequence of the present invention using systems based on steroid hormones is also contemplated. For example, a glucocorticoid-mediated induction system is used (Aoyama and Chua (1997) The Plant Journal 11: 605-612) and gene expression is induced by application of a glucocorticoid, for example a synthetic glucocorticoid, preferably dexamethasone, preferably at a concentration ranging from 0.1 mM to 1 mM, more preferably from 10 mM to 100 mM. For the purposes of the present invention, the luciferase gene sequences are replaced by a nucleic acid sequence of the invention to form an expression cassette having a nucleic acid sequence of the invention under the control of six copies of the GAL4 upstream activating sequences fused to the 35S minimal promoter. This is carried out using methods well known in the art. The trans-acting factor comprises the GAL4 DNA-binding domain (Keegan et al. (1986) Science 231: 699-704) fused to the transactivating domain of the herpes viral protein VP16 (Triezenberg et al. (1988) Genes Devel. 2: 718-729) fused to the hormone-binding domain of the rat glucocorticoid receptor (Picard et al. (1988) Cell 54: 1073-1080). The expression of the fusion protein is controlled by any promoter suitable for expression in plants known in the art or described here. This expression cassette is also comprised in the plant comprising a nucleic acid sequence of the invention fused to the 6×GAL4/minimal promoter. Thus, tissue- or organ-specificity of the fusion protein is achieved leading to inducible tissue- or organ-specificity of the insecticidal toxin.

[0235] g. Root Specific Expression:

[0236] Another pattern of gene expression is root expression. A suitable root promoter is the promoter of the maize metallothionein-like (MTL) gene described by de Framond (FEBS 290: 103-106 (1991)) and also in U.S. Pat. No. 5,466,785, incorporated herein by reference. This “MTL” promoter is transferred to a suitable vector such as pCGN1761ENX for the insertion of a selected gene and subsequent transfer of the entire promoter-gene-terminator cassette to a transformation vector of interest.

[0237] h. Wound-Inducible Promoters:

[0238] Wound-inducible promoters may also be suitable for gene expression. Numerous such promoters have been described (e.g. Xu et al. Plant Molec. Biol. 22: 573-588 (1993), Logemann et al. Plant Cell 1: 151-158 (1989), Rohrmeier & Lehle, Plant Molec. Biol. 22: 783-792 (1993), Firek et al. Plant Molec. Biol. 22: 129-142 (1993), Warner et al. Plant J. 3: 191-201 (1993)) and all are suitable for use with the instant invention. Logemann et al. describe the 5′ upstream sequences of the dicotyledonous potato wunl gene. Xu et al. show that a wound-inducible promoter from the dicotyledon potato (pin2) is active in the monocotyledon rice. Further, Rohrmeier & Lehle describe the cloning of the maize Wipl cDNA which is wound induced and which can be used to isolate the cognate promoter using standard techniques. Similar, Firek et al. and Warner et al. have described a wound-induced gene from the monocotyledon Asparagus officinalis, which is expressed at local wound and pathogen invasion sites. Using cloning techniques well known in the art, these promoters can be transferred to suitable vectors, fused to the genes pertaining to this invention, and used to express these genes at the sites of plant wounding.

[0239] i. Pith-Preferred Expression:

[0240] Patent Application WO 93/07278, which is herein incorporated by reference, describes the isolation of the maize trpA gene, which is preferentially expressed in pith cells. The gene sequence and promoter extending up to −1726 bp from the start of transcription are presented. Using standard molecular biological techniques, this promoter, or parts thereof, can be transferred to a vector such as pCGN1761 where it can replace the 35S promoter and be used to drive the expression of a foreign gene in a pith-preferred manner. In fact, fragments containing the pith-preferred promoter or parts thereof can be transferred to any vector and modified for utility in transgenic plants.

[0241] j. Leaf-Specific Expression:

[0242] A maize gene encoding phosphoenol carboxylase (PEPC) has been described by Hudspeth & Grula (Plant Molec Biol 12: 579-589 (1989)). Using standard molecular biological techniques the promoter for this gene can be used to drive the expression of any gene in a leaf-specific manner in transgenic plants.

[0243] k. Pollen-Specific Expression:

[0244] WO 93/07278 describes the isolation of the maize calcium-dependent protein kinase (CDPK) gene which is expressed in pollen cells. The gene sequence and promoter extend up to 1400 bp from the start of transcription. Using standard molecular biological techniques, this promoter or parts thereof, can be transferred to a vector such as pCGN1761 where it can replace the 35S promoter and be used to drive the expression of a nucleic acid sequence of the invention in a pollen-specific manner.

[0245] 2. Transcriptional Terminators

[0246] A variety of transcriptional terminators are available for use in expression cassettes. These are responsible for the termination of transcription beyond the transgene and correct mRNA polyadenylation. Appropriate transcriptional terminators are those that are known to function in plants and include the CaMV 35S terminator, the tml terminator, the nopaline synthase terminator and the pea rbcS E9 terminator. These can be used in both monocotyledons and dicotyledons. In addition, a gene's native transcription terminator may be used.

[0247] 3. Sequences for the Enhancement or Regulation of Expression

[0248] Numerous sequences have been found to enhance gene expression from within the transcriptional unit and these sequences can be used in conjunction with the genes of this invention to increase their expression in transgenic plants.

[0249] Various intron sequences have been shown to enhance expression, particularly in monocotyledonous cells. For example, the introns of the maize Adhl gene have been found to significantly enhance the expression of the wild-type gene under its cognate promoter when introduced into maize cells. Intron 1 was found to be particularly effective and enhanced expression in fusion constructs with the chloramphenicol acetyltransferase gene (Callis et al., Genes Develop. 1: 1183-1200 (1987)). In the same experimental system, the intron from the maize bronze1 gene had a similar effect in enhancing expression. Intron sequences have been routinely incorporated into plant transformation vectors, typically within the non-translated leader.

[0250] A number of non-translated leader sequences derived from viruses are also known to enhance expression, and these are particularly effective in dicotyledonous cells. Specifically, leader sequences from Tobacco Mosaic Virus (TMV, the “W-sequence”), Maize Chlorotic Mottle Virus (MCMV), and Alfalfa Mosaic Virus (AMV) have been shown to be effective in enhancing expression (e.g. Gallie et al. Nucl. Acids Res. 15: 8693-8711 (1987); Skuzeski et al. Plant Molec. Biol. 15: 65-79 (1990)). Other leader sequences known in the art include but are not limited to: picornavirus leaders, for example, EMCV leader (Encephalomyocarditis 5′ noncoding region) (Elroy-Stein, O., Fuerst, T. R., and Moss, B. PNAS USA 86:6126-6130 (1989)); potyvirus leaders, for example, TEV leader (Tobacco Etch Virus) (Allison et al., 1986); MDMV leader (Maize Dwarf Mosaic Virus); Virology 154:9-20); human immunoglobulin heavy-chain binding protein (BiP) leader, (Macejak, D. G., and Sarnow, P., Nature 353: 90-94 (1991); untranslated leader from the coat protein mRNA of alfalfa mosaic virus (AMV RNA 4), (Jobling, S. A., and Gehrke, L., Nature 325:622-625 (1987); tobacco mosaic virus leader (TMV), (Gallie, D. R. et al., Molecular Biology of RNA, pages 237-256 (1989); and Maize Chlorotic Mottle Virus leader (MCMV) (Lommel, S. A. et al., Virology 81:382-385 (1991). See also, Della-Cioppa et al., Plant Physiology 84:965-968 (1987).

[0251] In addition to incorporating one or more of the aforementioned elements into the 5′ regulatory region of a target expression cassette of the invention, other elements peculiar to the target expression cassette may also be incorporated. Such elements include but are not limited to a minimal promoter. By minimal promoter it is intended that the basal promoter elements are inactive or nearly so without upstream activation. Such a promoter has low background activity in plants when there is no transactivator present or when enhancer or response element binding sites are absent. One minimal promoter that is particularly useful for target genes in plants is the Bz1 minimal promoter, which is obtained from the bronze1 gene of maize. The Bz1 core promoter is obtained from the “myc” mutant Bz1-luciferase construct pBz1LucR98 via cleavage at the Nhel site located at −53 to −58. Roth et al., Plant Cell 3: 317 (1991). The derived Bz1 core promoter fragment thus extends from −53 to +227 and includes the Bz1 intron-1 in the 5′ untranslated region. Also useful for the invention is a minimal promoter created by use of a synthetic TATA element. The TATA element allows recognition of the promoter by RNA polymerase factors and confers a basal level of gene expression in the absence of activation (see generally, Mukumoto (1993) Plant Mol Biol 23: 995-1003; Green (2000) Trends Biochem Sci 25: 59-63)

[0252] 4. Targeting of the Gene Product Within the Cell

[0253] Various mechanisms for targeting gene products are known to exist in plants and the sequences controlling the functioning of these mechanisms have been characterized in some detail. For example, the targeting of gene products to the chloroplast is controlled by a signal sequence found at the amino terminal end of various proteins which is cleaved during chloroplast import to yield the mature protein (e.g. Comai et al. J. Biol. Chem. 263: 15104-15109 (1988)). These signal sequences can be fused to heterologous gene products to effect the import of heterologous products into the chloroplast (van den Broeck, et al. Nature 313: 358-363 (1985)). DNA encoding for appropriate signal sequences can be isolated from the 5′ end of the cDNAs encoding the RUBISCO protein, the CAB protein, the EPSP synthase enzyme, the GS2 protein and many other proteins which are known to be chloroplast localized. See also, the section entitled “Expression With Chloroplast Targeting” in Example 37 of U.S. Pat. No. 5,639,949.

[0254] Other gene products are localized to other organelles such as the mitochondrion and the peroxisome (e.g. Unger et al. Plant Molec. Biol. 13: 411-418 (1989)). The cDNAs encoding these products can also be manipulated to effect the targeting of heterologous gene products to these organelles. Examples of such sequences are the nuclear-encoded ATPases and specific aspartate amino transferase isoforms for mitochondria. Targeting cellular protein bodies has been described by Rogers et al. (Proc. Natl. Acad. Sci. USA 82: 6512-6516 (1985)).

[0255] In addition, sequences have been characterized which cause the targeting of gene products to other cell compartments. Amino terminal sequences are responsible for targeting to the ER, the apoplast, and extracellular secretion from aleurone cells (Koehler & Ho, Plant Cell 2: 769-783 (1990)). Additionally, amino terminal sequences in conjunction with carboxy terminal sequences are responsible for vacuolar targeting of gene products (Shinshi et al. Plant Molec. Biol. 14: 357-368 (1990)).

[0256] By the fusion of the appropriate targeting sequences described above to transgene sequences of interest it is possible to direct the transgene product to any organelle or cell compartment. For chloroplast targeting, for example, the chloroplast signal sequence from the RUBISCO gene, the CAB gene, the EPSP synthase gene, or the GS2 gene is fused in frame to the amino terminal ATG of the transgene. The signal sequence selected should include the known cleavage site, and the fusion constructed should take into account any amino acids after the cleavage site which are required for cleavage. In some cases this requirement may be fulfilled by the addition of a small number of amino acids between the cleavage site and the transgene ATG or, alternatively, replacement of some amino acids within the transgene sequence. Fusions constructed for chloroplast import can be tested for efficacy of chloroplast uptake by in vitro translation of in vitro transcribed constructions followed by in vitro chloroplast uptake using techniques described by Bartlett et al. In: Edelmann et al. (Eds.) Methods in Chloroplast Molecular Biology, Elsevier pp 1081-1091 (1982) and Wasmann et al. Mol. Gen. Genet. 205: 446-453 (1986). These construction techniques are well known in the art and are equally applicable to mitochondria and peroxisomes.

[0257] The above-described mechanisms for cellular targeting can be utilized not only in conjunction with their cognate promoters, but also in conjunction with heterologous promoters so as to effect a specific cell-targeting goal under the transcriptional regulation of a promoter that has an expression pattern different to that of the promoter from which the targeting signal derives.

C. Construction of Plant Transformation Vectors

[0258] Numerous transformation vectors available for plant transformation are known to those of ordinary skill in the plant transformation arts, and the genes pertinent to this invention can be used in conjunction with any such vectors. The selection of vector will depend upon the preferred transformation technique and the target species for transformation. For certain target species, different antibiotic or herbicide selection markers may be preferred. Selection markers used routinely in transformation include the nptll gene, which confers resistance to kanamycin and related antibiotics (Messing & Vierra. Gene 19: 259-268 (1982); Bevan et al., Nature 304:184-187 (1983)), the bar gene, which confers resistance to the herbicide phosphinothricin (White et al., Nucl. Acids Res 18: 1062 (1990), Spencer et al. Theor. Appl. Genet 79: 625-631 (1990)), the hph gene, which confers resistance to the antibiotic hygromycin (Blochinger & Diggelmann, Mol Cell Biol 4: 2929-2931), and the dhfr gene, which confers resistance to methatrexate (Bourouis et al., EMBO J. 2(7): 1099-1104 (1983)), the EPSPS gene, which confers resistance to glyphosate (U.S. Pat. Nos. 4,940,935 and 5,188,642), and the mannose-6-phosphate isomerase gene, which provides the ability to metabolize mannose (U.S. Pat. Nos. 5,767,378 and 5,994,629).

[0259] 1. Vectors Suitable for Agrobacterium Transformation

[0260] Many vectors are available for transformation using Agrobacterium tumefaciens. These typically carry at least one T-DNA border sequence and include vectors such as pBIN19 (Bevan, Nucl. Acids Res. (1984)). Below, the construction of two typical vectors suitable for Agrobacterium transformation is described.

[0261] a. pCIB200 and pCIB2001:

[0262] The binary vectors pCIB200 and pCIB2001 are used for the construction of recombinant vectors for use with Agrobacterium and are constructed in the following manner. pTJS75kan is created by Narl digestion of pTJS75 (Schmidhauser & Helinski, J. Bacteriol. 164: 446-455 (1985)) allowing excision of the tetracycline-resistance gene, followed by insertion of an Accl fragment from pUC4K carrying an NPTII (Messing & Vierra, Gene 19: 259-268 (1982): Bevan et al., Nature 304: 184-187 (1983): McBride et al., Plant Molecular Biology 14: 266-276 (1990)). XhoI linkers are ligated to the EcoRV fragment of PCIB7 which contains the left and right T-DNA borders, a plant selectable nos/nptlI chimeric gene and the pUC polylinker (Rothstein et al., Gene 53: 153-161 (1987)), and the XhoI-digested fragment are cloned into SalI-digested pTJS75kan to create pCIB200 (see also EP 0 332 104, example 19). pCIB200 contains the following unique polylinker restriction sites: EcoRI, SstI, KpnI, BgmlI, Xbal, and SalI. pCIB2001 is a derivative of pCIB200 created by the insertion into the polylinker of additional restriction sites. Unique restriction sites in the polylinker of pCIB2001 are EcoRI, SstI, KpnI, BglII, Xbal, SalI, MluI, BclI, AvrlI, ApaI, HpaI, and StuI. pCIB2001, in addition to containing these unique restriction sites also has plant and bacterial kanamycin selection, left and right T-DNA borders for Agrobacterium-mediated transformation, the RK2-derived trfA function for mobilization between E. coli and other hosts, and the OriT and OriV functions also from RK2. The pCIB2001 polylinker is suitable for the cloning of plant expression cassettes containing their own regulatory signals.

[0263] b. pCIB10 and Hygromycin Selection Derivatives Thereof:

[0264] The binary vector pCIB10 contains a gene encoding kanamycin resistance for selection in plants and T-DNA right and left border sequences and incorporates sequences from the wide host-range plasmid pRK252 allowing it to replicate in both E. coli and Agrobacterium. Its construction is described by Rothstein et at (Gene 53: 153-161 (1987)). Various derivatives of pCIB10 are constructed which incorporate the gene for hygromycin B phosphotransferase described by Gritz et al. (Gene 25: 179-188 (1983)). These derivatives enable selection of transgenic plant cells on hygromycin only (pCIB743), or hygromycin and kanamycin (pCIB715, pCIB717).

[0265] 2. Vectors Suitable for Non-Agrobacterium Transformation

[0266] Transformation without the use of Agrobacterium tumefaciens circumvents the requirement for T-DNA sequences in the chosen transformation vector and consequently vectors lacking these sequences can be utilized in addition to vectors such as the ones described above which contain T-DNA sequences. Transformation techniques that do not rely on Agrobacterium include transformation via particle bombardment, protoplast uptake (e.g. PEG and electroporation) and microinjection. The choice of vector depends largely on the preferred selection for the species being transformed. Below, the construction of typical vectors suitable for non-Agrobacterium transformation is described.

[0267] a. pCIB3064:

[0268] pCIB3064 is a pUC-derived vector suitable for direct gene transfer techniques in combination with selection by the herbicide basta (or phosphinothricin). The plasmid pCIB246 comprises the CaMV 35S promoter in operational fuson to the E. coli GUS gene and the CaMV 35S transcriptional terminator and is described in the PCT published application WO 93/07278. The 35S promoter of this vector contains two ATG sequences 5′ of the start site. These sites are mutated using standard PCR techniques in such a way as to remove the ATGs and generate the restriction sites SspI and PvulI. The new restriction sites are 96 and 37 bp away from the unique SalI site and 101 and 42 bp away from the actual start site. The resultant derivative of pCIB246 is designated pCIB3025. The GUS gene is then excised from pCIB3025 by digestion with SalI and SacI, the termini rendered blunt and religated to generate plasmid pCIB3060. The plasmid pJIT82 is obtained from the John Innes Centre, Norwich and the a 400 bp SmaI fragment containing the bar gene from Streptomyces vifidochromogenes is excised and inserted into the HpaI site of pCIB3060 (Thompson et al. EMBO J 6: 2519-2523 (1987)). This generated pCIB3064, which comprises the bar gene under the control of the CaMV 35S promoter and terminator for herbicide selection, a gene for ampicillin resistance (for selection in E. coli) and a polylinker with the unique sites SphI, Pstl, HindIII, and BamHI. This vector is suitable for the cloning of plant expression cassettes containing their own regulatory signals.

[0269] b. pSOG19 and pSOG35:

[0270] pSOG35 is a transformation vector that utilizes the E. coli gene dihydrofolate reductase (DFR) as a selectable marker conferring resistance to methotrexate. PCR is used to amplify the 35S promoter (−800 bp), intron 6 from the maize Adh1 gene (−550 bp) and 18 bp of the GUS untranslated leader sequence from pSOG10. A 250-bp fragment encoding the E. coli dihydrofolate reductase type II gene is also amplified by PCR and these two PCR fragments are assembled with a SacI-Pstl fragment from pB1221 (Clontech) which comprises the pUC19 vector backbone and the nopaline synthase terminator. Assembly of these fragments generates pSOG19 which contains the 35S promoter in fusion with the intron 6 sequence, the GUS leader, the DHFR gene and the nopaline synthase terminator. Replacement of the GUS leader in pSOG19 with the leader sequence from Maize Chlorotic Mottle Virus (MCMV) generates the vector pSOG35. pSOG19 and pSOG35 carry the pUC gene for ampicillin resistance and have HindIII, SphI, Pstl and EcoRI sites available for the cloning of foreign substances.

[0271] 3. Vector Suitable for Chloroplast Transformation

[0272] For expression of a nucleotide sequence of the present invention in plant plastids, plastid transformation vector pPH143 (WO 97/32011, example 36) is used. The nucleotide sequence is inserted into pPH143 thereby replacing the PROTOX coding sequence. This vector is then used for plastid transformation and selection of transformants for spectinomycin resistance. Alternatively, the nucleotide sequence is inserted in pPH143 so that it replaces the aadH gene. In this case, transformants are selected for resistance to PROTOX inhibitors.

D. Transformation

[0273] Once a nucleic acid sequence of the invention has been cloned into an expression system, it is transformed into a plant cell. The receptor and target expression cassettes of the present invention can be introduced into the plant cell in a number of art-recognized ways. Methods for regeneration of plants are also well known in the art. For example, Ti plasmid vectors have been utilized for the delivery of foreign DNA, as well as direct DNA uptake, liposomes, electroporation, microinjection, and microprojectiles. In addition, bacteria from the genus Agrobacterium can be utilized to transform plant cells. Below are descriptions of representative techniques for transforming both dicotyledonous and monocotyledonous plants, as well as a representative plastid transformation technique.

[0274] 1. Transformation of Dicotyledons

[0275] Transformation techniques for dicotyledons are well known in the art and include Agrobacterium-based techniques and techniques that do not require Agrobacterium. Non-Agrobacterium techniques involve the uptake of exogenous genetic material directly by protoplasts or cells. This can be accomplished by PEG or electroporation mediated uptake, particle bombardment-mediated delivery, or microinjection. Examples of these techniques are described by Paszkowski et al., EMBO J 3: 2717-2722 (1984), Potrykus et al., Mol. Gen. Genet. 199: 169-177 (1985), Reich et al., Biotechnology 4: 1001-1004 (1986), and Klein et al., Nature 327: 70-73 (1987). In each case the transformed cells are regenerated to whole plants using standard techniques known in the art.

[0276]Agrobacterium-mediated transformation is a preferred technique for transformation of dicotyledons because of its high efficiency of transformation and its broad utility with many different species. Agrobacterium transformation typically involves the transfer of the binary vector carrying the foreign DNA of interest (e.g. pCIB200 or pCIB2001) to an appropriate Agrobacterium strain which may depend of the complement of vir genes carried by the host Agrobacterium strain either on a co-resident Ti plasmid or chromosomally (e.g. strain CIB542 for pCIB200 and pCIB2001 (Uknes et al. Plant Cell 5: 159-169 (1993)). The transfer of the recombinant binary vector to Agrobacterium is accomplished by a triparental mating procedure using E. coli carrying the recombinant binary vector, a helper E. coli strain which carries a plasmid such as pRK2013 and which is able to mobilize the recombinant binary vector to the target Agrobacterium strain. Alternatively, the recombinant binary vector can be transferred to Agrobacterium by DNA transformation (Höfgen & Willmitzer, Nucl. Acids Res. 16: 9877 (1988)).

[0277] Transformation of the target plant species by recombinant Agrobacterium usually involves co-cultivation of the Agrobacterium with explants from the plant and follows protocols well known in the art. Transformed tissue is regenerated on selectable medium carrying the antibiotic or herbicide resistance marker present between the binary plasmid T-DNA borders.

[0278] Another approach to transforming plant cells with a gene involves propelling inert or biologically active particles at plant tissues and cells. This technique is disclosed in U.S. Pat. Nos. 4,945,050, 5,036,006, and 5,100,792 all to Sanford et al. Generally, this procedure involves propelling inert or biologically active particles at the cells under conditions effective to penetrate the outer surface of the cell and afford incorporation within the interior thereof. When inert particles are utilized, the vector can be introduced into the cell by coating the particles with the vector containing the desired gene. Alternatively, the target cell can be surrounded by the vector so that the vector is carried into the cell by the wake of the particle. Biologically active particles (e.g., dried yeast cells, dried bacterium or a bacteriophage, each containing DNA sought to be introduced) can also be propelled into plant cell tissue.

[0279] 2. Transformation of Monocotyledons

[0280] Transformation of most monocotyledon species has now also become routine. Preferred techniques include direct gene transfer into protoplasts using PEG or electroporation techniques, and particle bombardment into callus tissue. Transformations can be undertaken with a single DNA species or multiple DNA species (i.e. co-transformation) and both these techniques are suitable for use with this invention. Co-transformation may have the advantage of avoiding complete vector construction and of generating transgenic plants with unlinked loci for the gene of interest and the selectable marker, enabling the removal of the selectable marker in subsequent generations, should this be regarded desirable. However, a disadvantage of the use of co-transformation is the less than 100% frequency with which separate DNA species are integrated into the genome (Schocher et al. Biotechnology 4: 1093-1096 (1986)).

[0281] Patent Applications EP 0 292 435, EP 0 392 225, and WO 93/07278 describe techniques for the preparation of callus and protoplasts from an elite inbred line of maize, transformation of protoplasts using PEG or electroporation, and the regeneration of maize plants from transformed protoplasts. Gordon-Kamm et al. (Plant Cell 2: 603-618 (1990)) and Fromm et al. (Biotechnology 8: 833-839 (1990)) have published techniques for transformation of A188-derived maize line using particle bombardment. Furthermore, WO 93/07278 and Koziel et al. (Biotechnology 11: 194-200 (1993)) describe techniques for the transformation of elite inbred lines of maize by particle bombardment. This technique utilizes immature maize embryos of 1.5-2.5 mm length excised from a maize ear 14-15 days after pollination and a PDS-1000He Biolistics device for bombardment.

[0282] Transformation of rice can also be undertaken by direct gene transfer techniques utilizing protoplasts or particle bombardment. Protoplast-mediated transformation has been described for Japonica-types and Indica-types (Zhang et al. Plant Cell Rep 7: 379-384 (1988); Shimamoto et al. Nature 338: 274-277 (1989); Datta et al. Biotechnology 8: 736-740 (1990)). Both types are also routinely transformable using particle bombardment (Christou et al. Biotechnology 9: 957-962 (1991)). Furthermore, WO 93/21335 describes techniques for the transformation of rice via electroporation.

[0283] Patent Application EP 0 332 581 describes techniques for the generation, transformation and regeneration of Pooideae protoplasts. These techniques allow the transformation of Dactylis and wheat. Furthermore, wheat transformation has been described by Vasil et al. (Biotechnology 10: 667-674 (1992)) using particle bombardment into cells of type C long-term regenerable callus, and also by Vasil et al. (Biotechnology11:

[0284]1553-1558 (1993)) and Weeks et al. (Plant Physiol. 102: 1077-1084 (1993)) using particle bombardment of immature embryos and immature embryo-derived callus. A preferred technique for wheat transformation, however, involves the transformation of wheat by particle bombardment of immature embryos and includes either a high sucrose or a high maltose step prior to gene delivery. Prior to bombardment, any number of embryos (0.75-1 mm in length) are plated onto MS medium with 3% sucrose (Murashiga & Skoog, Physiologia Plantarum 15: 473-497 (1962)) and 3 mg/l 2,4-D for induction of somatic embryos, which is allowed to proceed in the dark. On the chosen day of bombardment, embryos are removed from the induction medium and placed onto the osmoticum (i.e. induction medium with sucrose or maltose added at the desired concentration, typically 15%). The embryos are allowed to plasmolyze for 2-3 hours and are then bombarded. Twenty embryos per target plate is typical, although not critical. An appropriate gene-carrying plasmid (such as pCIB3064 or pSG35) is precipitated onto micrometer size gold particles using standard procedures. Each plate of embryos is shot with the DuPont Biolistics®) helium device using a burst pressure of ˜1000 psi using a standard 80 mesh screen. After bombardment, the embryos are placed back into the dark to recover for about 24 hours (still on osmoticum). After 24 hrs, the embryos are removed from the osmoticum and placed back onto induction medium where they stay for about a month before regeneration. Approximately one month later the embryo explants with developing embryogenic callus are transferred to regeneration medium (MS+1 mg/liter NAA, 5 mg/liter GA), further containing the appropriate selection agent (10 mg/l basta in the case of pCIB3064 and 2 mg/l methotrexate in the case of pSOG35). After approximately one month, developed shoots are transferred to larger sterile containers known as “GA7s” which contain half-strength MS, 2% sucrose, and the same concentration of selection agent.

[0285] Tranformation of monocotyledons using Agrobacterium has also been described. See, WO 94/00977 and U.S. Pat. No. 5,591,616, both of which are incorporated herein by reference. See also, Negrotto et al., Plant Cell Reports 19: 798-803 (2000), incorporated herein by reference.

[0286] For this example, rice (Oryza sativa) is used for generating transgenic plants. Various rice cultivars can be used (Hiei et al., 1994, Plant Journal 6:271-282; Dong et al., 1996, Molecular Breeding 2:267-276; Hiei et al., 1997, Plant Molecular Biology, 35:205-218). Also, the various media constituents described below may be either varied in quantity or substituted. Embryogenic responses are initiated and/or cultures are established from mature embryos by culturing on MS-CIM medium (MS basal salts, 4.3 g/liter; B5 vitamins (200×), 5 ml/liter; Sucrose, 30 g/liter; proline, 500 mg/liter; glutamine, 500 mg/liter; casein hydrolysate, 300 mg/liter; 2,4-D (1 mg/ml), 2 ml/liter; adjust pH to 5.8 with 1 N KOH; Phytagel, 3 g/liter). Either mature embryos at the initial stages of culture response or established culture lines are inoculated and co-cultivated with the Agrobacterium tumefaciens strain LBA4404 (Agrobacterium) containing the desired vector construction. Agrobacterium is cultured from glycerol stocks on solid YPC medium (100 mg/L spectinomycin and any other appropriate antibiotic) for ˜2 days at 28° C. Agrobacterium is re-suspended in liquid MS-CIM medium. The Agrobacterium culture is diluted to an OD600 of 0.2-0.3 and acetosyringone is added to a final concentration of 200 uM. Acetosyringone is added before mixing the solution with the rice cultures to induce Agrobacterium for DNA transfer to the plant cells. For inoculation, the plant cultures are immersed in the bacterial suspension. The liquid bacterial suspension is removed and the inoculated cultures are placed on co-cultivation medium and incubated at 22° C. for two days. The cultures are then transferred to MS-CIM medium with Ticarcillin (400 mg/liter) to inhibit the growth of Agrobacterium. For constructs utilizing the PMI selectable marker gene (Reed et al., In Vitro Cell. Dev. Biol.-Plant 37:127-132), cultures are transferred to selection medium containing Mannose as a carbohydrate source (MS with 2% Mannose, 300 mg/liter Ticarcillin) after 7 days, and cultured for 3-4 weeks in the dark. Resistant colonies are then transferred to regeneration induction medium (MS with no 2,4-D, 0.5 mg/liter IAA, 1 mg/liter zeatin, 200 mg/liter timentin 2% Mannose and 3% Sorbitol) and grown in the dark for 14 days. Proliferating colonies are then transferred to another round of regeneration induction media and moved to the light growth room. Regenerated shoots are transferred to GA7 containers with GA7-1 medium (MS with no hormones and 2% Sorbitol) for 2 weeks and then moved to the greenhouse when they are large enough and have adequate roots. Plants are transplanted to soil in the greenhouse (To generation) grown to maturity, and the T₁ seed is harvested.

[0287] 3. Transformation of Plastids

[0288] Seeds of Nicotiana tabacum c.v. ‘Xanthienc’ are germinated seven per plate in a 1” circular array on T agar medium and bombarded 12-14 days after sowing with 1 μm tungsten particles (M10, Biorad, Hercules, CA) coated with DNA from plasmids pPH143 and pPH145 essentially as described (Svab, Z. and Maliga, P. (1993) PNAS 90, 913-917). Bombarded seedlings are incubated on T medium for two days after which leaves are excised and placed abaxial side up in bright light (350-500 μmol photons/m²/s) on plates of RMOP medium (Svab, Z., Hajdukiewicz, P. and Maliga, P. (1990) PNAS 87, 8526-8530) containing 500 μg/ml spectinomycin dihydrochloride (Sigma, St. Louis, Mo.). Resistant shoots appearing underneath the bleached leaves three to eight weeks after bombardment are subcloned onto the same selective medium, allowed to form callus, and secondary shoots isolated and subcloned. Complete segregation of transformed plastid genome copies (homoplasmicity) in independent subclones is assessed by standard techniques of Southern blotting (Sambrook et al., (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor). BamHI/EcoRI-digested total cellular DNA (Mettler, I. J. (1987) Plant Mol Biol Reporter 5, 346349) is separated on 1% Tris-borate (TBE) agarose gels, transferred to nylon membranes (Amersham) and probed with ³²P-labeled random primed DNA sequences corresponding to a 0.7 kb BamHI/HindIII DNA fragment from pC8 containing a portion of the rps{fraction (7/12)}plastid targeting sequence. Homoplasmic shoots are rooted aseptically on spectinomycin-containing MS/IBA medium (McBride, K. E. et al. (1994) PNAS 91, 7301-7305) and transferred to the greenhouse.

V. Breeding and Seed Production A. Breeding

[0289] The plants obtained via tranformation with a nucleic acid sequence of the present invention can be any of a wide variety of plant species, including those of monocots and dicots; however, the plants used in the method of the invention are preferably selected from the list of agronomically important target crops set forth supra. The expression of a gene of the present invention in combination with other characteristics important for production and quality can be incorporated into plant lines through breeding. Breeding approaches and techniques are known in the art. See, for example, Welsh J. R., Fundamentals of Plant Genetics and Breeding, John Wiley & Sons, NY (1981); Crop Breeding, Wood D. R. (Ed.) American Society of Agronomy Madison, Wis. (1983); Mayo O., The Theory of Plant Breeding, Second Edition, Clarendon Press, Oxford (1987); Singh, D.P., Breeding for Resistance to Diseases and Insect Pests, Springer-Verlag, NY (1986); and Wricke and Weber, Quantitative Genetics and Selection Plant Breeding, Walter de Gruyter and Co., Berlin (1986).

[0290] The genetic properties engineered into the transgenic seeds and plants described above are passed on by sexual reproduction or vegetative growth and can thus be maintained and propagated in progeny plants. Generally said maintenance and propagation make use of known agricultural methods developed to fit specific purposes such as tilling, sowing or harvesting, Specialized processes such as hydroponics or greenhouse technologies can also be applied. As the growing crop is vulnerable to attack and damages caused by insects or infections as well as to competition by weed plants, measures are undertaken to control weeds, plant diseases, insects, nematodes, and other adverse conditions to improve yield. These include mechanical measures such a tillage of the soil or removal of weeds and infected plants, as well as the application of agrochemicals such as herbicides, fungicides, gametocides, nematicides, growth regulants, ripening agents and insecticides.

[0291] Use of the advantageous genetic properties of the transgenic plants and seeds according to the invention can further be made in plant breeding, which aims at the development of plants with improved properties such as tolerance of pests, herbicides, or stress, improved nutritional value, increased yield, or improved structure causing less loss from lodging or shattering. The various breeding steps are characterized by well-defined human intervention such as selecting the lines to be crossed, directing pollination of the parental lines, or selecting appropriate progeny plants. Depending on the desired properties, different breeding measures are taken. The relevant techniques are well known in the art and include but are not limited to hybridization, inbreeding, backcross breeding, multiline breeding, variety blend, interspecific hybridization, aneuploid techniques, etc. Hybridization techniques also include the sterilization of plants to yield male or female sterile plants by mechanical, chemical, or biochemical means. Cross pollination of a male sterile plant with pollen of a different line assures that the genome of the male sterile but female fertile plant will uniformly obtain properties of both parental lines. Thus, the transgenic seeds and plants according to the invention can be used for the breeding of improved plant lines, that for example, increase the effectiveness of conventional methods such as herbicide or pesticide treatment or allow one to dispense with said methods due to their modified genetic properties. Alternatively new crops with improved stress tolerance can be obtained, which, due to their optimized genetic “equipment”, yield harvested product of better quality than products that were not able to tolerate comparable adverse developmental conditions.

B. Seed Production

[0292] In seed production, germination quality and uniformity of seeds are essential product characteristics. As it is difficult to keep a crop free from other crop and weed seeds, to control seedborne diseases, and to produce seed with good germination, fairly extensive and well-defined seed production practices have been developed by seed producers, who are experienced in the art of growing, conditioning and marketing of pure seed. Thus, it is common practice for the farmer to buy certified seed meeting specific quality standards instead of using seed harvested from his own crop. Propagation material to be used as seeds is customarily treated with a protectant coating comprising herbicides, insecticides, fungicides, bactericides, nematicides, molluscicides, or mixtures thereof. Customarily used protectant coatings comprise compounds such as captan, carboxin, thiram (TMTD®), methalaxyl (Apron®), and pirimiphos-methyl (Actellic®). If desired, these compounds are formulated together with further carriers, surfactants or application-promoting adjuvants customarily employed in the art of formulation to provide protection against damage caused by bacterial, fungal or animal pests. The protectant coatings may be applied by impregnating propagation material with a liquid formulation or by coating with a combined wet or dry formulation. Other methods of application are also possible such as treatment directed at the buds or the fruit.

[0293] VI. Alteration of Expression of Nucleic Acid Molecules

[0294] For example, the alteration in expression of the nucleic acid molecules of the present invention is achieved in one of the following ways:

[0295] A. “Sense” Suppression

[0296] Alteration of the expression of a nucleotide sequence of the present invention, preferably reduction of its expression, is obtained by “sense” suppression (referenced in e.g. Jorgensen et al. (1996) Plant Mol. Biol. 31, 957-973). In this case, the entirety or a portion of a nucleotide sequence of the present invention is comprised in a DNA molecule. The DNA molecule is preferably operatively linked to a promoter functional in a cell comprising the target gene, preferably a plant cell, and introduced into the cell, in which the nucleotide sequence is expressible. The nucleotide sequence is inserted in the DNA molecule in the “sense orientation”, meaning that the coding strand of the nucleotide sequence can be transcribed. In a preferred embodiment, the nucleotide sequence is fully translatable and all the genetic information comprised in the nucleotide sequence, or portion thereof, is translated into a polypeptide. In another preferred embodiment, the nucleotide sequence is partially translatable and a short peptide is translated. In a preferred embodiment, this is achieved by inserting at least one premature stop codon in the nucleotide sequence, which bring translation to a halt. In another more preferred embodiment, the nucleotide sequence is transcribed but no translation product is being made. This is usually achieved by removing the start codon, e.g. the “ATG”, of the polypeptide encoded by the nucleotide sequence. In a further preferred embodiment, the DNA molecule comprising the nucleotide sequence, or a portion thereof, is stably integrated in the genome of the plant cell. In another preferred embodiment, the DNA molecule comprising the nucleotide sequence, or a portion thereof, is comprised in an extrachromosomally replicating molecule.

[0297] In transgenic plants containing one of the DNA molecules described immediately above, the expression of the nucleotide sequence corresponding to the nucleotide sequence comprised in the DNA molecule is preferably reduced. Preferably, the nucleotide sequence in the DNA molecule is at least 70% identical to the nucleotide sequence the expression of which is reduced, more preferably it is at least 80% identical, yet more preferably at least 90% identical, yet more preferably at least 95% identical, yet more preferably at least 99% identical.

[0298] B. “Anti-Sense” Suppression

[0299] In another preferred embodiment, the alteration of the expression of a nucleotide sequence of the present invention, preferably the reduction of its expression is obtained by “anti-sense” suppression. The entirety or a portion of a nucleotide sequence of the present invention is comprised in a DNA molecule. The DNA molecule is preferably operatively linked to a promoter functional in a plant cell, and introduced in a plant cell, in which the nucleotide sequence is expressible. The nucleotide sequence is inserted in the DNA molecule in the “anti-sense orientation”, meaning that the reverse complement (also called sometimes non-coding strand) of the nucleotide sequence can be transcribed. In a preferred embodiment, the DNA molecule comprising the nucleotide sequence, or a portion thereof, is stably integrated in the genome of the plant cell. In another preferred embodiment the DNA molecule comprising the nucleotide sequence, or a portion thereof, is comprised in an extrachromosomally replicating molecule. Several publications describing this approach are cited for further illustration (Green, P. J. et al., Ann. Rev. Biochem. 55:569-597 (1986); van der Krol, A. R. et al, Antisense Nuc. Acids & Proteins, pp. 125-141 (1991); Abel, P. P. et al., PNAS. USA 86:6949-6952 (1989); Ecker, J. R. et al., Proc. Natl. Acad. Sci. USA 83:5372-5376 (August 1986)).

[0300] In transgenic plants containing one of the DNA molecules described immediately above, the expression of the nucleotide sequence corresponding to the nucleotide sequence comprised in the DNA molecule is preferably reduced. Preferably, the nucleotide sequence in the DNA molecule is at least 70% identical to the nucleotide sequence the expression of which is reduced, more preferably it is at least 80% identical, yet more preferably at least 90% identical, yet more preferably at least 95% identical, yet more preferably at least 99% identical. Antisense suppression of the RARI nucleic acid molecules of the invention is more specifically described below in Example 5.

[0301] C. Homologous Recombination

[0302] In another preferred embodiment, at least one genomic copy corresponding to a nucleotide sequence of the present invention is modified in the genome of the plant by homologous recombination as further illustrated in Paszkowski et al., EMBO Journal 7:4021-26 (1988). This technique uses the property of homologous sequences to recognize each other and to exchange nucleotide sequences between each by a process known in the art as homologous recombination. Homologous recombination can occur between the chromosomal copy of a nucleotide sequence in a cell and an incoming copy of the nucleotide sequence introduced in the cell by transformation. Specific modifications are thus accurately introduced in the chromosomal copy of the nucleotide sequence. In one embodiment, the regulatory elements of the nucleotide sequence of the present invention are modified. Such regulatory elements are easily obtainable by screening a genomic library using the nucleotide sequence of the present invention, or a portion thereof, as a probe. The existing regulatory elements are replaced by different regulatory elements, thus altering expression of the nucleotide sequence, or they are mutated or deleted, thus abolishing the expression of the nucleotide sequence. In another embodiment, the nucleotide sequence is modified by deletion of a part of the nucleotide sequence or the entire nucleotide sequence, or by mutation. Expression of a mutated polypeptide in a plant cell is also contemplated in the present invention. More recent refinements of this technique to disrupt endogenous plant genes have been described (Kempin et al., Nature 389:802-803 (1997) and Miao and Lam, Plant J., 7:359-365 (1995).

[0303] In another preferred embodiment, a mutation in the chromosomal copy of a nucleotide sequence is introduced by transforming a cell with a chimeric oligonucleotide composed of a contiguous stretch of RNA and DNA residues in a duplex conformation with double hairpin caps on the ends. An additional feature of the oligonucleotide is for example the presence of 2′-O-methylation at the RNA residues. The RNA/DNA sequence is designed to align with the sequence of a chromosomal copy of a nucleotide sequence of the present invention and to contain the desired nucleotide change. For example, this technique is further illustrated in U.S. Pat. No. 5,501,967 and Zhu et al. (1999) Proc. Natl. Acad. Sci. USA 96: 8768-8773.

[0304] D. Ribozymes

[0305] In a further embodiment, the RNA coding for a polypeptide of the present invention is cleaved by a catalytic RNA, or ribozyme, specific for such RNA. The ribozyme is expressed in transgenic plants and results in reduced amounts of RNA coding for the polypeptide of the present invention in plant cells, thus leading to reduced amounts of polypeptide accumulated in the cells. This method is further illustrated in U.S. Pat. No. 4,987,071.

[0306] E. Dominant-Negative Mutants

[0307] In another preferred embodiment, the activity of the polypeptide encoded by the nucleotide sequences of this invention is changed. This is achieved by expression of dominant negative mutants of the proteins in transgenic plants, leading to the loss of activity of the endogenous protein.

[0308] F. Aptamers

[0309] In a further embodiment, the activity of polypeptide of the present invention is inhibited by expressing in transgenic plants nucleic acid ligands, so-called aptamers, which specifically bind to the protein. Aptamers are preferentially obtained by the SELEX (Systematic Evolution of Ligands by EXponential Enrichment) method. In the SELEX method, a candidate mixture of single stranded nucleic acids having regions of randomized sequence is contacted with the protein and those nucleic acids having an increased affinity to the target are partitioned from the remainder of the candidate mixture. The partitioned nucleic acids are amplified to yield a ligand enriched mixture. After several iterations a nucleic acid with optimal affinity to the polypeptide is obtained and is used for expression in transgenic plants. This method is further illustrated in U.S. Pat. No. 5,270,163.

[0310] G. Zinc Finger Proteins

[0311] A zinc finger protein that binds a nucleotide sequence of the present invention or to its regulatory region is also used to alter expression of the nucleotide sequence. Preferably, transcription of the nucleotide sequence is reduced or increased. Zinc finger proteins are for example described in Beerli et al. (1998) PNAS PNAS 95:14628-14633., or in WO 95/19431, WO 98/54311, or WO 96/06166, all incorporated herein by reference in their entirety.

[0312] H. dsRNA

[0313] Alteration of the expression of a nucleotide sequence of the present invention is also obtained by dsRNA interference as described for example in WO 99/32619, WO 99/53050 or WO 99/61631, all incorporated herein by reference in their entirety. In another preferred embodiment, the alteration of the expression of a nucleotide sequence of the present invention, preferably the reduction of its expression, is obtained by double-stranded RNA (dsRNA) interference. The entirety or, preferably a portion of a nucleotide sequence of the present invention is comprised in a DNA molecule. The size of the DNA molecule is preferably from 100 to 1000 nucleotides or more; the optimal size to be determined empirically. Two copies of the identical DNA molecule are linked, separated by a spacer DNA molecule, such that the first and second copies are in opposite orientations. In the preferred embodiment, the first copy of the DNA molecule is in the reverse complement (also known as the non-coding strand) and the second copy is the coding strand; in the most preferred embodiment, the first copy is the coding strand, and the second copy is the reverse complement. The size of the spacer DNA molecule is preferably 200 to 10,000 nucleotides, more preferably 400 to 5000 nucleotides and most preferably 600 to 1500 nucleotides in length. The spacer is preferably a random piece of DNA, more preferably a random piece of DNA without homology to the target organism for dsRNA interference, and most preferably a functional intron which is effectively spliced by the target organism. The two copies of the DNA molecule separated by the spacer are operatively linked to a promoter functional in a plant cell, and introduced in a plant cell, in which the nucleotide sequence is expressible. In a preferred embodiment, the DNA molecule comprising the nucleotide sequence, or a portion thereof, is stably integrated in the genome of the plant cell.

[0314] In another preferred embodiment the DNA molecule comprising the nucleotide sequence, or a portion thereof, is comprised in an extrachromosomally replicating molecule. Several publications describing this approach are cited for further illustration (Waterhouse et al. (1998) PNAS 95:13959-13964; Chuang and Meyerowitz (2000) PNAS 97:49854990; Smith et al. (2000) Nature 407:319-320). Alteration of the expression of a nucleotide sequence by dsRNA interference is also described in, for example WO 99/32619, WO 99/53050 or WO 99/61631, all incorporated herein by reference in their entirety

[0315] In transgenic plants containing one of the DNA molecules described immediately above, the expression of the nucleotide sequence corresponding to the nucleotide sequence comprised in the DNA molecule is preferably reduced. Preferably, the nucleotide sequence in the DNA molecule is at least 70% identical to the nucleotide sequence the expression of which is reduced, more preferably it is at least 80% identical, yet more preferably at least 90% identical, yet more preferably at least 95% identical, yet more preferably at least 99% identical.

[0316] I. Insertion of a DNA Molecule (Insertional Mutagenesis)

[0317] In another preferred embodiment, a DNA molecule is inserted into a chromosomal copy of a nucleotide sequence of the present invention, or into a regulatory region thereof. Preferably, such DNA molecule comprises a transposable element capable of transposition in a plant cell, such as e.g. Ac/Ds, Em/Spm, mutator. Alternatively, the DNA molecule comprises a T-DNA border of an Agrobacterium T-DNA. The DNA molecule may also comprise a recombinase or integrase recognition site which can be used to remove part of the DNA molecule from the chromosome of the plant cell. Methods of insertional mutagenesis using T-DNA, transposons, oligonucleotides or other methods known to those skilled in the art are also encompassed. Methods of using T-DNA and transposon for insertional mutagenesis are described in Winkler et al. (1989) Methods Mol. Biol. 82:129-136 and Martienssen (1998) PNAS 95:2021-2026, incorporated herein by reference in their entireties.

[0318] J. Deletion Mutagenesis

[0319] In yet another embodiment, a mutation of a nucleic acid molecule of the present invention is created in the genomic copy of the sequence in the cell or plant by deletion of a portion of the nucleotide sequence or regulator sequence. Methods of deletion mutagenesis are known to those skilled in the art. See, for example, Miao et al, (1995) Plant J. 7:359. In yet another embodiment, this deletion is created at random in a large population of plants by chemical mutagenesis or irradiation and a plant with a deletion in a gene of the present invention is isolated by forward or reverse genetics. Irradiation with fast neutrons or gamma rays is known to cause deletion mutations in plants (Silverstone et al, (1998) Plant Cell, 10:155-169; Bruggemann et al., (1996) Plant J., 10:755-760; Redei and Koncz in Methods in Arabidopsis Research, World Scientific Press (1992), pp. 16-82). Deletion mutations in a gene of the present invention can be recovered in a reverse genetics strategy using PCR with pooled sets of genomic DNAs as has been shown in C. elegans (Liu et al., (1999), Genome Research, 9:859-867.). A forward genetics strategy would involve mutagenesis of a line displaying PTGS followed by screening the M2 progeny for the absence of PTGS. Among these mutants would be expected to be some that disrupt a gene of the present invention. This could be assessed by Southern blot or PCR for a gene of the present invention with genomic DNA from these mutants.

[0320] K. Overexpression in a Plant Cell

[0321] In yet another preferred embodiment, a nucleotide sequence of the present invention encoding a polypeptide is over-expressed. Examples of nucleic acid molecules and expression cassettes for over-expression of a nucleic acid molecule of the present invention are described above. Methods known to those skilled in the art of over-expression of nucleic acid molecules are also encompassed by the present invention.

[0322] In a preferred embodiment, the expression of the nucleotide sequence of the present invention is altered in every cell of a plant. This is for example obtained though homologous recombination or by insertion in the chromosome. This is also for example obtained by expressing a sense or antisense RNA, zinc finger protein or ribozyme under the control of a promoter capable of expressing the sense or antisense RNA, zinc finger protein or ribozyme in every cell of a plant. Constitutive expression, inducible, tissue-specific or developmentally-regulated expression are also within the scope of the present invention and result in a constitutive, inducible, tissue-specific or developmentally-regulated alteration of the expression of a nucleotide sequence of the present invention in the plant cell. Constructs for expression of the sense or antisense RNA, zinc finger protein or ribozyme, or for over-expression of a nucleotide sequence of the present invention, are prepared and transformed into a plant cell according to the teachings of the present invention, e.g. as described infra.

VII. Polypeptides

[0323] The present invention further relates to isolated polypeptides comprising the amino acid sequence of SEQ ID NO:2. In particular, isolated polypeptides comprising the amino acid sequence of SEQ ID NO:2, and variants having conservative amino acid modifications. One skilled in the art will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide or protein sequence which alters, adds or deletes a single amino acid or a small percent of amino acids in the encoded sequence is a “conservative modification” where the modification results in the substitution of an amino acid with a chemically similar amino acid. Conservative modified variants provide similar biological activity as the unmodified polypeptide. Conservative substitution tables listing functionally similar amino acids are known in the art. See Crighton (1984) Proteins, W.H. Freeman and Company.

[0324] In a preferred embodiment, a polypeptide having substantial similarity to a polypeptide sequence listed in even numbered SEQ ID NO:2-64, or exon, domain, or feature thereof, is an allelic variant of the polypeptide sequence listed in even numbered SEQ ID NO:2-64. In another preferred embodiment, a polypeptide having substantial similarity to a polypeptide sequence listed in even numbered SEQ ID NO:2-64, or exon, domain, or feature thereof, is a naturally occurring variant of the polypeptide sequence listed in even numbered SEQ ID NO:2-64. In another preferred embodiment, a polypeptide having substantial similarity to a polypeptide sequence listed in even numbered SEQ ID NO:2-64, or exon, domain, or feature thereof, is a polymorphic variant of the polypeptide sequence listed in even numbered SEQ ID NO:2-64.

[0325] In an alternate preferred embodiment, the sequence having substantial similarity contains a deletion or insertion of at least one amino acid. In a more preferred embodiment, the deletion or insertion is of less than about ten amino acids. In a most preferred embodiment, the deletion or insertion is of less than about three amino acids.

[0326] In a preferred embodiment, the sequence having substantial similarity encodes a substitution in at least one amino acid.

[0327] Embodiments of the present invention also contemplate an isolated polypeptide containing a polypeptide sequence including:

[0328] (f) a polypeptide sequence listed in even numbered SEQ ID NO:2-64, or exon, domain, or feature thereof;

[0329] (g) a polypeptide sequence having substantial similarity to (a);

[0330] (h) a polypeptide sequence encoded by a nucleotide sequence identical to or having substantial similarity to a nucleotide sequence listed in odd numbered SEQ ID NO:1-63, or an exon, domain, or feature thereof, or a sequence complementary thereto;

[0331] (i) a polypeptide sequence encoded by a nucleotide sequence capable of hybridizing under medium stringency conditions to a nucleotide sequence listed in odd numbered SEQ ID NO:1-63, or to a sequence complementary thereto; and

[0332] (j) A Functional Fragment of (a), (b), (c) or (d).

[0333] In another preferred embodiment, the polypeptide having substantial similarity is an allelic variant of a polypeptide sequence listed in even numbered SEQ ID NO:2-64, or a fragment, domain, repeat, feature, or chimeras thereof. In another preferred embodiment, the isolated nucleic acid includes a plurality of regions from the polypeptide sequence encoded by a nucleotide sequence identical to or having substantial similarity to a nucleotide sequence listed in odd numbered SEQ ID NO:1-63, or fragment, domain, or feature thereof, or a sequence complementary thereto.

[0334] In another preferred embodiment, the polypeptide is a polypeptide sequence listed in odd numbered SEQ ID NO:2-64. In another preferred embodiment, the polypeptide is a functional fragment or domain. In yet another preferred embodiment, the polypeptide is a chimera, where the chimera may include functional protein domains, including domains, repeats, post-translational modification sites, or other features. In a more preferred embodiment, the polypeptide is a plant polypeptide. In a more preferred embodiment, the plant is a dicot. In a more preferred embodiment, the plant is a gymnosperm. In a more preferred embodiment, the plant is a monocot. In a more preferred embodiment, the monocot is a cereal. In a more preferred embodiment, the cereal may be, for example, maize, wheat, barley, oats, rye, millet, sorghum, triticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum, and teosinte. In a most preferred embodiment, the cereal is rice.

[0335] In a preferred embodiment, the polypeptide is expressed in a specific location or tissue of a plant. In a more preferred embodiment, the location or tissue is for example, but not limited to, epidermis, vascular tissue, meristem, cambium, cortex or pith. In a most preferred embodiment, the location or tissue is leaf or sheath, root, flower, and developing ovule or seed. In a more preferred embodiment, the location or tissue may be, for example, epidermis, root, vascular tissue, meristem, cambium, cortex, pith, leaf, and flower. In a more preferred embodiment, the location or tissue is a seed.

[0336] In a preferred embodiment, the polypeptide sequence encoded by a nucleotide sequence having substantial similarity to a nucleotide sequence listed in odd numbered SEQ ID NO:1-63 or a fragment, domain, or feature thereof or a sequence complementary thereto, includes a deletion or insertion of at least one nucleotide. In a more preferred embodiment, the deletion or insertion is of less than about thirty nucleotides. In a most preferred embodiment, the deletion or insertion is of less than about five nucleotides.

[0337] In a preferred embodiment, the polypeptide sequence encoded by a nucleotide sequence having substantial similarity to a nucleotide sequence listed in odd numbered SEQ ID NO:1-63, or fragment, domain, or feature thereof or a sequence complementary thereto, includes a substitution of at least one codon. In a more preferred embodiment, the substitution is conservative.

[0338] In a preferred embodiment, the polypeptide sequences having substantial similarity to the polypeptide sequence listed in even numbered SEQ ID NO:2-64, or a fragment, domain, repeat, feature, or chimeras thereof includes a deletion or insertion of at least one amino acid.

[0339] The polypeptides of the invention, fragments thereof or variants thereof can comprise any number of contiguous amino acid residues from a polypeptide of the invention, wherein the number of residues is selected from the group of integers consisting of from 10 to the number of residues in a full-length polypeptide of the invention. Preferably, the portion or fragment of the polypeptide is a functional protein. The present invention includes active polypeptides having specific activity of at least 20%, 30%, or 40%, and preferably at least 505, 60%, or 70%, and most preferably at least 805, 90% or 95% that of the native (non-synthetic) endogenous polypeptide. Further, the substrate specificity (k_(cat)K_(m)) is optionally substantially similar to the native (non-synthetic), endogenous polypeptide. Typically the K_(m) will be at least 30%, 40%, or 50% of the native, endogenous polypeptide; and more preferably at least 605, 70%, 80%, or 90%. Methods of assaying and quantifying measures of activity and substrate specificity are well known to those of skill in the art.

[0340] The isolated polypeptides of the present invention will elicit production of an antibody specifically reactive to a polypeptide of the present invention when presented as an immunogen. Therefore, the polypeptides of the present invention can be employed as immunogens for constructing antibodies immunoreactive to a protein of the present invention for such purposes, but not limited to, immunoassays or protein purification techniques. Immunoassays for determining binding are well known to those of skill in the art such as, but not limited to, ELISAs or competitive immunoassays.

[0341] Embodiments of the present invention also relate to chimeric polypeptides encoded by the isolated nucleic acid molecules of the present disclosure including a chimeric polypeptide containing a polypeptide sequence encoded by an isolated nucleic acid containing a nucleotide sequence including:

[0342] (g) a nucleotide sequence listed in odd numbered SEQ ID NO:1-63, or exon, domain, or feature thereof;

[0343] (h) a nucleotide sequence having substantial similarity to (a);

[0344] (i) a nucleotide sequence capable of hybridizing to (a);

[0345] (j) a nucleotide sequence complementary to (a), (b) or (c); and

[0346] (k) a nucleotide sequence which is the reverse complement of (a), (b) or (c);

[0347] (l) or a functional fragment thereof.

[0348] A polypeptide containing a polypeptide sequence encoded by an isolated nucleic acid containing a nucleotide sequence, its complement, or its reverse complement, encoding a polypeptide including a polypeptide sequence including:

[0349] (g) a polypeptide sequence listed in even numbered SEQ ID NO:2-64, or a domain, repeat, feature, or chimeras thereof;

[0350] (h) a polypeptide sequence having substantial similarity to (a);

[0351] (i) a polypeptide sequence encoded by a nucleotide sequence identical to or having substantial similarity to a nucleotide sequence listed in odd numbered SEQ ID NO:1-63, or an exon, domain, or feature thereof, or a sequence complementary thereto;

[0352] (j) a polypeptide sequence encoded by a. nucleotide sequence capable of hybridizing under medium stringency conditions to a nucleotide sequence listed in odd numbered SEQ ID NO:1-63, or to a sequence complementary thereto; and

[0353] (k) a functional fragment of (a), (b), (c) or (d);

[0354] (l) or a functional fragment thereof.

[0355] The isolated nucleic acid molecules of the present invention are useful for expressing a polypeptide of the present invention in a recombinantly engineered cell such as a bacteria, yeast, insect, mammalian or plant cell. The cells produce the polypeptide in a non-natural condition (e.g. in quantity, composition, location and/or time) because they have been genetically altered to do so. Those skilled in the art are knowledgeable in the numerous expression systems available for expression of nucleic acids encoding a protein of the present invention, and will not be described in detail below.

[0356] Briefly, the expression of isolated nucleic acids encoding a polypeptide of the invention will typically be achieved, for example, by operably linking the nucleic acid or cDNA to a promoter (constitutive or regulatable) followed by incorporation into an expression vector. The vectors are suitable for replication and/or integration in either prokaryotes or eukaryotes. Commonly used expression vectors comprise transcription and translation terminators, initiation sequences and promoters for regulation of the expression of the nucleic acid molecule encoding the polypeptide. To obtain high levels of expression of the cloned nucleic acid molecule, it is desirable to use expression vectors comprising a strong promoter to direct transcription, a ribosome binding site for translation initiation, and a transcription/translation terminator. One skilled in the art will recognize that modifications may be made to the polypeptide of the present invention without diminishing its biological activity. Some modifications may be made to facilitate the cloning, expression or incorporation of the polypeptide of the invention into a fusion protein. Such modification are well known in the art and include, but are not limited to, a methionine added at the amino terminus to provide an initiation site, or additional amino acids (e.g. poly Histadine) placed on either terminus to create conveniently located purification sequences. Restricton sites or termination codons can also be introduced into the vector.

[0357] In a preferred embodiment, the expression vector includes one or more elements such as, for example, but not limited to, a promoter-enhancer sequence, a selection marker sequence, an origin of replication, an epitope-tag encoding sequence, or an affinity purification-tag encoding sequence. In a more preferred embodiment, the promoter-enhancer sequence may be, for example, the CaMV 35S promoter, the CaMV 19S promoter, the tobacco PR-la promoter, the ubiquitin promoter, and the phaseolin promoter. In another embodiment, the promoter is operable in plants, and more preferably, a constitutive or inducible promoter. In another preferred embodiment, the selection marker sequence encodes an antibiotic resistance gene. In another preferred embodiment, the epitope-tag sequence encodes V5, the peptide Phe-His-His-Thr-Thr, hemagglutinin, or glutathione-S-transferase. In another preferred embodiment the affinity purification-tag sequence encodes a polyamino acid sequence or a polypeptide. In a more preferred embodiment, the polyamino acid sequence is polyhistidine. In a more preferred embodiment, the polypeptide is chitin binding domain or glutathione-S-transferase. In a more preferred embodiment, the affinity purification-tag sequence comprises an intein encoding sequence.

[0358] Prokaryotic cells may be used a host cells, for example, but not limited to, Escherichia coli, and other microbial strains known to those in the art. Methods for expressing proteins in prokaryotic cells are well known to those in the art and can be found in many laboratory manuals such as Molecular Cloning: A Laboratory Manual, by J. Sambrook et al. (1989, Cold Spring Harbor Laboratory Press). A variety of promoters, ribosome binding sites, and operators to control expression are available to those skilled in the art, as are selectable markers such as antibiotic resistance genes. The type of vector chosen is to allow for optimal growth and expression in the selected cell type.

[0359] A variety of eukaryotic expression systems are available such as, but not limited to, yeast, insect cell lines, plant cells and mammalian cells. Expression and synthesis of heterologous proteins in yeast is well known (see Sherman et al., Methods in Yeast Genetics, Cold Spring Harbor Laboratory Press, 1982). Commonly used yeast strains widely used for production of eukaryotic proteins are Saccharomyces cerevisiae and Pichia pastoris, and vectors, strains and protocols for expression are available from commercial suppliers (e.g., Invitrogen).

[0360] Mammalian cell systems may be transfected with expression vectors for production of proteins. Many suitable host cell lines are available to those in the art, such as, but not limited to the HEK293, BHK21 and CHO cells lines. Expression vectors for these cells can include expression control sequences such as an origin of replication, a promoter, ( e.g., the CMV promoter, a HSV tk promoter or phosphoglycerate kinase (pgk) promoter), an enhancer, and protein processing sites such as ribosome binding sites, RNA splice sites, polyadenylation sites, and transcription terminator sequences. Other animal cell lines useful for the production of proteins are available commercially or from depositories such as the American Type Culture Collection.

[0361] Expression vectors for expressing proteins in insect cells are usually derived from the SF9 baculovirus or other viruses known in the art. A number of suitable insect cell lines are available including but not limited to, mosquito larvae, silkworm, armyworm, moth and Drosophila cell lines.

[0362] Methods of transfecting animal and lower eukaryotic cells are known. Numerous methods are used to make eukaryotic cells competent to introduce DNA such as but not limited to: calcium phosphate precipitation, fusion of the recipient cell with bacterial protoplasts containing the DNA, treatment of the recipient cells with liposomes containing the DNA, DEAE dextrin, electroporation, biolistics, and microinjection of the DNA directly into the cells. Tranfected cells are cultured using means well known in the art (see, Kuchler, R. J., Biochemical Methods in Cell Culture and Virology, Dowden, Hutchinson and Ross, Inc. 1997).

[0363] Once a polypeptide of the present invention is expressed it may be isolated and purified from the cells using methods known to those skilled in the art. The purification process may be monitored using Western blot techniques or radioimmunoassay or other standard immunoassay techniques. Protein purification techniques are commonly known and used by those in the art (see R. Scopes, Protein Purification: Principles and Practice, Springer-Verlag, New York 1982: Deutscher, Guide to Protein Purification, Academic Press (1990). Embodiments of the present invention provide a method of producing a recombinant protein in which the expression vector includes one or more elements including a promoter-enhancer sequence, a selection marker sequence, an origin of replication, an epitope-tag encoding sequence, and an affinity purification-tag encoding sequence. In one preferred embodiment, the nucleic acid construct includes an epitope-tag encoding sequence and the isolating step includes use of an antibody specific for the epitope-tag. In another preferred embodiment, the nucleic acid construct contains a polyamino acid encoding sequence and the isolating step includes use of a resin comprising a polyamino acid binding substance, preferably where the polyamino acid is polyhistidine and the polyamino binding resin is nickel-charged agarose resin. In yet another preferred embodiment, the nucleic acid construct contains a polypeptide encoding sequence and the isolating step includes the use of a resin containing a polypeptide binding substance, preferably where the polypeptide is a chitin binding domain and the resin contains chitin-sepharose.

[0364] The polypeptides of the present invention cam be synthesized using non-cellular synthetic methods known to those in the art. Techniques for solid phase synthesis are described by Barany and Mayfield, Solid-Phase Peptide Synthesis, pp. 3-284 in the Peptides: Analysis, Synthesis, Biology, Vol.2 Special Methods in Peptide Synthesis, Part A; Merrifield, et al., J. Am. Chem. Soc. 85:2149-56 (1963) and Stewart et al., Solid Phase Peptide Synthesis, 2^(nd) ed. Pierce Chem. Co., Rockford, Ill. (1984).

[0365] The present invention further provides a method for modifying (i.e. increasing or decreasing) the concentration or composition of the polypeptides of the invention in a plant or part thereof. Modification can be effected by increasing or decreasing the concentration and/or the composition (i.e. the ration of the polypeptides of the present invention) in a plant. The method comprised introducing into a plant cell with an expression cassette comprising a nucleic acid molecule of the present invention, or an nucleic acid encoding a RAR1 sequence as described above to obtain a transformed plant cell or tissue, culturing the transformed plant cell or tissue. The nucleic acid molecule can be under the regulation of a constitutive or inducible promoter. The method can further comprise inducing or repressing expression of a nucleic acid molecule of a sequence in the plant for a time sufficient to modify the concentration and/or composition in the plant or plant part.

[0366] A plant or plant part having modified expression of a nucleic acid molecule of the invention can be analyzed and selected using methods known to those skilled in the art such as, but not limited to, Southern blot, DNA sequencing, or PCR analysis using primers specific to the nucleic acid molecule and detecting amplicons produced therefrom.

[0367] In general, concentration or composition in increased or decreased by at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% relative to a native control plant, plant part or cell lacking the expression cassette.

[0368] The invention will be further described by reference to the following detailed examples. These examples are provided for purposes of illustration only, and are not intended to be limiting unless otherwise specified.

EXAMPLES

[0369] Standard recombinant DNA and molecular cloning techniques used here are well known in the art and are described by J. Sambrook, et al., Molecular Cloning: A Laboratory Manual, 3d Ed., Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press (2001); by T. J. Silhavy, M. L. Berman, and L. W. Enquist, Experiments with Gene Fusions, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1984) and by Ausubel, F. M. et al., Current Protocols in Molecular Biology, New York, John Wiley and Sons Inc., (1988), Reiter, et al., Methods in Arabidopsis Research, World Scientific Press (1992), and Schultz et al., Plant Molecular Biology Manual, Kluwer Academic Publishers (1998).

Example 1 Identification of Nucleic Acid Molecules (cDNAs) from Rice

[0370] A list of over 250 genes from diverse plant species was compiled based on their adjudged potential to confer an agronomic trait in a crop plant. Genes were identified by the species name and the name of the gene. For example the Arabidopsis ethylene insensitive 2 (EIN2) gene is referred to as AtEIN2. The traits of interest included, but were not limited to, disease resistance, abiotic stress tolerance, enhanced nutritional value, yield, flowering time, and hormone response. These genes were conceptually translated, and the resultant predicted peptides encoded by these genes (defined as “queries”) were used to search for similar genes in the Syngenta/Myriad Genetics proprietary rice genomic database ( Myriad contigs version 8). Similarity searching was done using the TBlastN algorithm and both a Blosum 62 and a Pam70 matrix, with other parameters at default settings. Similar results were obtained with the two matrices. Searches were carried out on the TimeLogic DeCypher server at TMRI in San Diego, or locally, using the same database. High scoring genomic contig hits (P value <10⁻¹⁰) were designated as containing homologs; the highest scoring genomic contig was in most, but not all, cases designated as containing the rice ortholog. Orthologs were given an “Os” designation in front of their gene. Thus, the rice ortholog to the AtEIN2 query was designated OsEIN2. In exceptional cases, more than one putative rice ortholog to a single query was identified and further pursued (eg. OsEIN2, OsEIN2b, etc. . . ).

[0371] The rice ortholog thus identified resided in a contiguous stretch (“genomic contig”) of rice genomic DNA sequence. Various commercially available gene prediction algorithms (FGENESH, GenMark, GenMarkHMM, Genescan, GeneWise) were used to predict partial or full-length cDNAs of the rice orthologs. Predicted cDNAs (sequences in SBI predicted cDNAs.doc; conceptual translations in SBI predicted peptides) were used to search a database of assembled consensus sequences of sequenced rice cDNA library clones (“cDNA contigs”) using BlastN with default settings on the TimeLogic DeCypher server at TMRI in San Diego. cDNA contigs with identity or near-identity to the predicted cDNA were identified and DNA from the longest cDNA clone was obtained from stocks at Torrey Mesa Research Institute (“TMRI”) (San Diego). Additional cDNAs were obtained from designing primers to the full-length, or partial predicted cDNAs, amplifying the cDNAs by PCR from rice cDNA libraries or first-strand cDNA, and cloning them by conventional TA cloning or Gateway™ technology (using pCR2.1TOPO or pDONR201 vectors (Invitrogen), respectively). In either case, cDNA clones were sequenced to confirm their identity. These cDNAs constitute a subset of those included in the SBI predicted cDNAs and are physical DNA clones that have been validated by sequencing (Listing 3) and by comparing them against the original target rice ortholog sequence using similarity search algorithms as outlined above. BLASTX—compares a translation of the DNA sequencing in 6 frames to a protein database. The protein database used was GenBank non-reduntant peptides.

[0372] To assign function to these genes, the conceptual translations of the sequences in SBI Predicted cDNAs.doc and in SBI cDNAs.doc were used to search the SwissProt protein database and GenPept non-redundant conceptual translation database using the BlastP algorithm at default settings. Functional assignments to rice cDNAs, based on similarity for the corresponding peptides to proteins and genes of known function, are included in Tables 1-4 and the Examples below.

Example 2 Cloning and Sequence of Nucleic Acid Molecules from Rice

[0373] The longest clones corresponding to full-length contigs identified in the rice cDNA library were streaked out and DNA. was made from these cells. Alternatively, oligonucleotide primers to the 5′ and 3′ ends end of the predicted gene, and inclusive of the predicted start and stop codons, were used to PCR amplify the gene from rice first strand cDNA or the cDNA library. In some instances, these PCR primers included additional 5′ sequences for Gateway™ recombination-based cloning (invitrogen). PCR amplification was carried out using the HF Advantage II (Clonetech) or EXPAND (Roche) PCR kits according to the manufacturer's instructions. PCR products were cloned into pCR2.1-TOPO or pDONR201 according to the manufacturer's instructions (Invitrogen).

[0374] DNA preps for 24 independent clones was miniprepped following the manufacturer's instructions. DNA was subjected to sequencing analysis using the BigDyeT™ Terminator Kit according to manufacturer's instructions (ABI). Sequencing made use of primers designed to both strands of the predicted gene. Alternatively, the DNA was transformed into a strain with an active transposon, followed by sequencing of random independent colonies using primers from each of the transposon ends using the EZ::TN™ TET-1 Insertion kit (Epicentre). All sequencing data were analyzed and assembled using the Phred/Phrap/Consed software package (University of Washington) to an error ratio equal to or less than 10⁻⁴ at the consensus sequence level.

[0375] Consensus sequences were validated as being intact and the correct gene in several ways. The coding region was checked for being full length (predicted start and stop codons present) and uninterrupted (no internal stop codons). Alignment with the gene prediction and BLAST analysis was used to ascertain if this was the intended target gene. Most of the cDNA clones included 5′ and 3′ untranslated sequences, providing additional evidence that these were indeed full length. In some instances, silent or missense changes were observed (changes encoding the same or a different amino acid, respectively). These changes were most likely due to sequencing errors in the genomic reference sequence, although errors generated during PCR amplification could not be completely ruled out for clones generated using PCR.

[0376] Full-length cDNA clones or full-length open reading frames generated by PCR were cloned into custom-made binary destination vectors using Gateway™ recombination-based cloning per the manufacturer's instructions (Invitrogen). Alternatively, PCR products were cloned using conventional restriction enzyme-based cloning.

Example 3 Expression Vectors and Tranformation of Plants

[0377] Binary destination vectors for plant transformation consist of a binary backbone and a T-DNA portion. The binary backbone contains the sequences necessary for selection and growth in Escherichia coli DH-5□ (Invitrogen) and Agrobacterium tumefaciens LBA4404, including the bacterial spectinomycin antibiotic resistance aadA gene from E. coli transposon Tn7, origins of replication for E. coli (ColE1) and A. tumefaciens (VS1), and the A. tumefaciens virG gene. The T-DNA portion was flanked by the right and left border sequences and includes the Positech™ (Syngenta) plant selectable marker and a gene expression cassette which varies depending on the application. The Positech™ plant selectable marker in this instance consists of a rice ACT1 (actin) promoter driving expression of the PMI (phosphomannose isomerase) gene, followed by the cauliflower mosaic virus transcriptional terminator, and confers resistance to mannose.

[0378] The gene expression cassette portion of the binary destination vectors varies depending on the application. In general, the cassette consists of a promoter designed to express the gene in certain tissues of the plant, followed by cloning sites (in some cases interrupted by a segment of spacer DNA), and finally by the A. tumefaciens nos 3′ end transcriptional terminator. The promoters used are designed to express the gene of interest in specific target tissues (eg. endosperm: maize ADPgpp or □-zein, or barley □-thionin; eg. embryo: maize globulin or oleosin; eg. aleurone: barley a-amylase; eg. root: maize MSR1 and MRS3; eg. green tissue: maize PEPC) or constitutively (eg. maize UBI plus intron), depending on the gene of interest. The cloning site contains either unique restriction enzyme sites (for conventional cloning) and/or a Gateway™ recombination-based cloning cassette (Invitrogen), in either the forward or reverse orientation. In gene expression cassettes designed for double-stranded interfering RNA (dsRNAi) production, the cloning site is divided by a spacer region (eg. first intron of the rice SH1 gene), thus permitting the cloning of two gene fragments, in the forward and reverse orientations respectively. dsRNAi and antisense are two technologies available for silencing genes of interest.

[0379] Transformation of the nucleic acid molecules of the present invention into plants is performed using methods described above in the Detailed Description.

Example 4 Abiotic Stress Tolerance cDNAs and Analysis

[0380] The function of the protein encoded by each abiotic stress tolerance gene is determined from analysis of the open reading frame (ORF) in each cDNA as described in Example 1. Table 1 describes the assigned functions for the abiotic stress tolerance genes described in this application. TABLE 1 Abiotic Stress Tolerance Genes SEQ ID Putative Function & Similar Homology Reference Gene Nos: Genes E value and % Homology ABF3 1-2 drought tolerance 1.00E−100 Hobo et al., Proc. Natl. TRAB1 from rice (Oryza Acad. Sci. U.S.A. 96 sativa) - bZIP transcription (26), 15348-15353 factor, interacts with VP1 (1999) transcription factor, a key 203/326 (62%) regulator of ABA response genes. ABA plant hormone mediates drought tolerance response. ASK1 3-4 drought & salt tolerance 1.00E−162 Yoon et al., Mol. Gen. Protein kinase SPK-3 Genet. 255 (4), 359-371 from soybean (Glycine (1997) max); upregulated by 279/365 (76%) drought and salt. ES147 5-6 salt tolerance 0 Galvez et al., Plant E5I47 protein kinase from Physiol. 103, 257-265 Lophopyrum elongatum; (1993) upregulated by salt stress. 365/442 (82%) FAD8 7-8 cold tolerance 0 Horiguchi et al., Fatty acid desaturase Physiol. Plantarum 96, from wheat (Triticum 275-283 (1996) aestivum); overexpression 300/353 (84%) of Arabidopsis thaliana gene confers cold tolerance. SAL1  9-10 salt tolerance 0 Peng and Verma, J. 3′(2′),5′-bisphosphate Biol. Chem. 270 (49), nucleotidase from rice 29105-29110 (1995) (Oryza sativa); 355/358 (99%) overexpression enhances salt tolerance

[0381] The abiotic stress tolerance genes are evaluated for their effect(s) in transformed plants by testing the transgenic transformed plants or progeny plants as compared with non-transgenic plants. The plants are tested for their altered tolerance cold, drought, salt and heat using methods known to those skilled in the art, and examples of such assays are described below.

[0382] Cold tolerance is tested by placing transgenic and non-transgenic plants of the same age in growth chambers at 5° C., with a 12 hr light/dark cycle, at 80% humidity for 72 hours. The plants are observed for enhanced tolerance or sensitivity to cold.

[0383] Tolerance to salt is measured by using any salt tolerance assay known to those skilled in the art. In particular, the salt tolerance assay is performed essentially as follows:

[0384] Seeds from transformed plants and untransformed parental lines are sown on filter paper soaked with Yoshida solution placed in petri dishes. After 7 days of growth in the climate chamber seedlings (about 4 cm shoot length and 4 cm root length) will be exposed to salt stress as follows: seedlings will be transferred to 24 well plates supplemented with Yoshida solution (control) or Yoshida solution enriched with two different salt concentrations (as below). To ensure the contact of the entire root with the solution a piece of moistened absorbent cotton is placed on top of the root within the well flooded with the solution. Alternatively, the seeds may be grown in sand as a growth medium.

[0385] Control: Yoshida Solution Without Supplementary Salt

[0386] 1) Yoshida solution enriched with NaCl 3.2 mg/l (48 mM)+CaCl₂ 3.6 mg/l (24 mM). This salt concentration evoked 50% growth reduction in shoot length.

[0387] 2) Yoshida solution enriched with NaCl 6.4 mg/l (96 mM)+CaCl₂ 7.1 mg/l (48 mM).

[0388] Tissue is harvested at: 0, 6, 12, 24, and 36 hours. After exposure, the seedlings are separated into shoots and roots, or whole seedlings (whichever you prefer) and then immediately frozen in liquid nitrogen for RNA extraction and analysis. Total RNA extraction is performed using any known method in the art such as, an RNA extraction kit from Qiagen.

[0389] Alternatively, seedlings are observed for enhanced or decreased tolerance to grown under salt stress as compared to the untransformed parental variety or line. Samples are also taken for analysis of protein expression. Yoshida Solutions Stock preparation Culture solution Final conc. Elem. Chemical names (g/10 L stock) (ml stock/10 L solutions) (mM (ppm)) (Macro) N NH₄NO₃ 914 12.5 1.43 mM (114 pm) P NaH₂PO₄.2H₂O 403 12.5 0.33 mM (51 ppm) K K₂SO₄ 714 12.5 0.51 mM (89 ppm) Ca CaCl₂ 886 12.5 1.0 mM (111 ppm) Mg MgSO₄.7H₂O 3240 12.5 1.6 mM (394 ppm) (Micro)* Mn MnCl₂.4H₂O 15-20 >0.01 mM Mo (NH₄)₆.MO₇O₂₄.4H₂O 1.5 1.5 × 10⁻⁴ mM B H₃BO₃ 12 0.02 mM Zn ZnSO₄.7H₂O 0.7 3 × 10⁻⁴ mM Cu CuSO₄.5H₂O 0.31 1.6 × 10⁻⁴ mM Citric acid 119 12.5 of mixture 0.071 mM (Iron) Fe Iron chelate 160 12.5

[0390] For drought tolerance, substitute 20% polyethylene glycol (PEG; MW 8000) for the salt solution.

Example 5 Disease Resistance Genes and Analysis

[0391] The function of the protein encoded by each disease resistance gene is determined from analysis of the open reading frame (ORF) in each cDNA as described in Example 1. Table 2 describes the assigned functions for the disease resistance genes described in this application. TABLE 2 Disease Resistance Genes Homology SEQ Putative Function Reference and Gene ID NO: and Similar Genes E value % Homology AOS2 11-12 disease resistance 1.00E−163 Sivasankar Allene oxide et al., synthase from unpublished tomato 271/418 (64%) (Lycopersicon esculentum); key jasmonic acid biosynthetic enzyme gene. BWMK1 13-14 disease resistance 0 He et al., Mol. MAP kinase from Plant Microbe rice (Oryza sativa); Interact. upregulated by 12: 1064-1073 pathogen infection. (1999). 505/506 (99%) DDE1 15-16 disease resistance 1.00E−170 Strassner et al., 12- unpublished oxophytodienoate 283/374 (75%) reductase 3 from tomato (Lycopersicon esculentum) - key jasmonic acid biosynthetic enzyme gene. ERF1 17-18 disease resistance 2.00E−36  Solano et al., Arabidopsis Genes Dev. thaliana ethylene 12(23): reponse factor 3703-3714 transcription factor. (1998) Ethylene plant 80/140 (57%) hormone mediates defense responses. JISP6 19-20 disease resistance   1E−126 Sasaki et al., Bowman Birk unpublished trypsin inhibitor 194/195 (99%) from rice (Oryza  61/145 (42%) sativa); induced by jasmonic acid, plant hormone mediating plant defense responses. LOX1 21-22 disease resistance 0 Peng et al., J. Lipoxygenase from Biol. Chem. rice (Oryza sativa) 269 (5), induced by 3755-3761 incompatible (1994) pathogen infection. 906/924 (98%) PIPLC1 23-24 disease resistance 0 Song and Phosphoinositide- Goodman, specific unpublished phospholipase C 562/599 (93%) from rice (Oryza sativa); upregulated by pathogen infection

[0392] Assays for testing disease resistance to a variety of pathogens known to those skilled in the art are performed on transgenic plants and non-transgenic parental lines to determine alteration in disease resistance.

[0393] For example, but by no means limiting, such disease resistance assays are performed essentially as described below.

[0394] Rice Detached Leaf Assay for Bacterial Blight

[0395] This example describes the disease resistance assay of the rice gene transformed rice plants and control plants using the detached leaf assays for bacterial blight (Xanthomonas oryzae pv otyzae (Xoo or Xanthomonas; Mmixture of isolates XOO 698 and PXO 112)). Transgenic plants are also compared to resistance of rice plants treated with Bion™.

[0396] 1. Rice seedlings are planted 1 seed per pot in 4 cm×4 cm pots with a mix of 50% peat and 50% John Innes Potting compost number 3 soil. Plants are checked twice daily and spot watered if soil appears dry on the surface. Plants are grown in a growth room (16 hour light cycle at a light intensity of 15000 μMol; 27° C. day 80% humidity; 20° C. night 90% humidity) until testing.

[0397] 2. Plants treated with Bion™ (formulation type and strength e.g. azibenzolar-s-methly 800 g/kg wettable powder) are subjected to soil drench application is used 7 days prior to inoculating with bacteria. The 4 cm×4 cm pots have a volume of 40 ml with a headspace of 4 ml for the solution. Thus, applying a 600 ppm solution to the top of the plants in the pots will result in a 60 ppm treatment. A 600 ppm solution comprises 60 mg active ingredient in 100 ml water. Dilutions from this solution are made for treatments with lower concentrations. Prior to application of Bion™, the plants to be treated are placed in saucers 2 cm deep and are not watered 24-hours pre treatment. The Bion™ application is made by pipetting 40 ml of the chemical solution onto the surface of the soil in each pot. After 24 hours post treatment the saucers are removed and normal watering regime is restored

[0398] 3. Xooanthomonas oryzae pv oryzae cultures for inoculation are produced from single isolate bacterial stocks (kept at 4° C. stored on) 2 days prior test date. Xooanthomonas oryzae pv oryzae bacterial cultures are grown in 500 ml nutrient broth. Bacteria are picked up on the tip of a sterile pipette and resuspended in 500 ml nutrient broth (recipe below). Cultures are incubated at 25° C. on a platform shaker (115 rpm) for between 1 and 4 days (typically flasks are used 2 days after introduction of the bacteria). Successful bacterial growth is indicated by the nutrient broth becoming opaque and a more intense yellow colour. Immediately before inoculation of leaf pieces flasks of Isolates XOO 698 (JH code K4214) and PXO 112 (JH code K4211) are mixed to produce a dual isolate inoculation.

[0399] 4. For the Xanthomonas detached leaf assay, plants approximately 12 weeks old are used. A total of 15 leaf samples are cut from randomly selected plants of each line of interest (i.e. transgenic event or non transgenic germplasm), or each individual treatment (i.e. combination of line and chemical application). A leaf sample is a section of the leaf between 5 cm and 6 cm long, and the width of the leaf wide, and may include the tip of the leaf. Multiple leaf samples can be obtained from one leaf. Leaf samples are always taken from the youngest fully expanded leaf available on the plant.

[0400] Control lines and treatments are included consisting of leaf 30 leaf samples from 12-week-old non-transgenic (wildtype) plants of the same variety as that used in the generation of the transgenic events and 30 leaf samples from Bion™ treated wildtype plants (12-week-old). As some level of senescence regularly occurs in detached leaf assays further plates of leaves that are only inoculated with nutrient broth (i.e. uninoculated controls) are also prepared. These plates consist of 30 leaf samples from wfildtype plants, 30 leaf samples from Bion™ treated wildtype plants and 15 leaf samples from 2 transgenic lines selected at random. These control plates allow assessors to clearly establish the difference in appearance between disease symptomology and unrelated senescence in the leaf samples.

[0401] 5. Leaf samples are placed adaxial side up onto petri dishes containing 1% tap water agar amended with 75 ppm benzimidazole. Leaf samples are fully randomised between plates with a maximum of 6 samples per plate.

[0402] 6. Leaf samples are inoculated individually with a syringe by twice injecting approximately 0.1 ml of Xooanthomonas oryzae pv ofyzae (isolates XOO 698 mixed with PXO 112) bacterial culture solution into the tip end of the leaf sample (one injection either side of the vascular bundle). Inoculations are completed in a laminar flow hood to reduce contamination of the bacterial cultures. After inoculation the plates are placed into a controlled environment incubator with conditions set at 32° C. day, 25° C. night and a 16 hour light cycle. A maximum humidity of 90% is maintained in the cabinet throughout the plate incubation time.

[0403] Assessments of disease development and senescence levels are completed every 48 hours, for up to 10 days after inoculation. Assessments made after 2 days for “spontaneous suicide” and every 3 days for curl, health and levels of “ooze.” The key indication of disease establishment within the leaf sample was the presence of yellow bacterial exudates (ooze) at one or both cut ends of the leaf. Lower incidence of exudates is a measure of decreased disease development and, hence, enhanced disease resistance and in the line(s) of interest resistance within the leaf sample.

[0404] The data for the blight assay is collated from the levels of ooze that is observed on the leaf pieces. Ooze is a symptom of XZanthomonas infection documented as occurring in detached leaf assays and is based on a method described by G. L. Xie (Plant Disease 82:1007-1011 (September 1998). Ooze manifests as a yellow exudated that occurs at the cut ends of an infected leaf. Leaf pieces are scored differently depending on if the ooze is observed at the inoculated end only or if the ooze had developed through the leaf and is also present at the opposing end of the leaf to the end innocuated. It is assumed that if ooze is observed at both ends, the leaf sample is exhibiting no resistance to the disease. If the inoculated end only exhibited ooze, there is some indication that the leaf piece is showing some resistance to the disease. If no ooze is observed at either end of the leaf piece there is an indication of strong resistance to the disease. Leaf pieces are scored as having presense or absense of ooze at each end (no quantification of the amount of ooze present). Transgenic plants expressing disease resistance genes show improved disease resistance and produce less ooze than wildtype plants.

[0405] Recipes

[0406] Nutrient broth for Xanthornonas oryzae pv oiyzae inoculum production 6.5 g Nutrient Broth (Oxoid CM1) into 500 ml Demonized Water. Stir until fully dissolved (about 5 minutes). Autoclave at 121° C. for 20 minutes.

[0407] Rice Assay for Rice Blast Disease (Caused by Pyricularia Grisea; Also Known as Magnaporthe Grisea)

[0408] This example describes the bioassay for resistance of RAR1 transgenic rice to rice blast Pyricularia grisea (strain K4005).

[0409] 1. Rice seedlings are planted 1 seed per pot in 4 cm×4 cm pots with a mix of 50% peat and 50% John Innes Potting compost number 3 soil. Plants are checked twice daily and spot watered if soil appears dry on the surface. Plants are grown in a growthroom (16 hour light cycle at a light intensity of 15000 μMol; 27° C. day 80% humidity; 20° C. night 90% humidity) until testing.

[0410] 2. Plants treated with Bion, are treated using a drench application 7 days prior to inoculation. The 4 cm×4 cm diameter pots have a volume of 150 mis with a headspace of 15 mls for the solution. Thus, applying a 600 ppm solution to the top of the plants in the pots will result in a 60 ppm treatment. A 600 ppm solution is made up of 60 mg active ingredient in 100 ml water. Make dilutions from that solution for treatments with lower concentrations.

[0411] 3. Pyricularia grisea inoculum is prepared from 5 day old single isolate stock plates (kept at 25° C. on rice leaf extract agar—recipe below) immediately before required for inoculation. 20 ml sterile deionised water is added to a plate of Pyricularia grisea, which is then rubbed with a small soft brush to encourage the spores into solution. The resulting spore and mycelium solution is then filtered through one layer of fine mesh muslin. Spores are counted in with using haemocytometer and the inoculum solution was diluted to produce a concentration of 200,000 spores/ml. The inoculum is used within one hour of production. It is recommended to allow 5 ml of inoculum per plate. Rice leaf extract agar for Pyricularia inoculum production: 45 g Czapek Dox Agar, 10 g Oxide Agar No.3, 1000 ml rice leaf extract. Extract 50 g of dried straw with 1000 ml of water at 100° C. for 1 hour. Autoclave at 121° C. for 20 minutes.

[0412] For the Pyricularia grisea detached leaf assay plants approximately 12 weeks old were used. A total of 15 leaf samples are cut from randomly selected plants of each line of interest (i.e. transgenic event or non transgenic germplasm), or each individual treatment (i.e. combination of line and chemical application). A leaf sample is a section of the leaf between 5 cm and 6 cm long, and the width of the leaf wide, and may include the tip of the leaf. Leaf pieces are placed so that both ends of the leaf were buried into the agar as this increases the green life of the leaf samples. Multiple leaf samples can be obtained from one leaf. Leaf samples are always taken from the youngest fully expanded leaf available on the plant. Control lines and treatments are included consisting of leaf 30 leaf samples from 12 week old non-transgenic (wildtype) plants of the same variety as that used in the generation of the transgenic events and 30 leaf samples from Bion™ treated wildtype plants (12 weeks old). As some level of senescence regularly occurs in detached leaf assays further plates of leaves that are inoculated with only sterile deionized water (i.e. uninoculated controls) were also prepared. These plates consisted of 30 leaf samples from wildtype plants, 30 leaf samples from Bion™ treated wildtype plants and 15 leaf samples from 2 transgenic lines selected at random. These control plates allow assessors to establish clearly the difference in appearance between disease symptomology and unrelated senescence in the leaf samples.

[0413] 5. Leaf samples are placed adaxial surface upwards onto petri dishes containing 1% tap water agar amended with 75 ppm benzimidazole. Leaf samples are fully randomised .between plates with a maximum of 6 samples per plate.

[0414] 6. Inoculum is sprayed onto the plates using a Devilbiss spray gun. Leaf pieces are sprayed to produce an equal coverage of droplets over the exposed leaf surface. The petri dish plate lids are replaced immediately and plates are incubated in a controlled environment cabinet for up to 8 days (conditions—14 hour light cycle; 24° C. day; 24° C. night constant 90% humidity).

[0415] 7. Plates are assessed for disease development (expressed as a estimated % disease coverage) and senescence levels every 48 hours for up to 8 days.

[0416] Medium for Xanthomonas otyzae pv oryzae Storage-Wakimoto Media

[0417] The data from the rice blast assay show that the transgenic lines assayed showed less disease coverage than the wildtype Kaybonnet rice line, demonstrating enhanced disease resistance in these lines. The wildtype treated with Bion™ showed the expected effect of decreased disease coverage.

[0418] This data clearly demonstrates that overexpression of the disease resistance gene in transgenic plants enhances disease resistance.

Example 6 Grain Quality and Nutritional Composition Genes and Analysis

[0419] The function of the protein encoded by each grain quality or nutritional composition gene is determined from analysis of the open reading frame (ORF) in each cDNA as described in Example 1. Table 3 describes the assigned functions for these genes described in this application. TABLE 3 Grain Quality and Nutritional Composition Genes SEQ Putative Function and Homology Reference and % Gene ID NO Similar Gene E value Homology BT1 25-26 starch level 8.00E−70  Sullivan et al., Plant Cell 3 Adenylate transporter (12), 1337-1348 (1991) from maize (Zea mays) - 165/305 (54%) brittle-1, key starch  53/165 (32%) biosynthesis protein  29/90 (32%) BTH1 27-28 thiamin level 1.00E−180 Theologis et al., Nature 408 Arabidopsis thaliana (6814), 816-820 (2000) phosphomethylpyrimidine 328/499 (65%) kinase - thiamin B vitamin biosynthetic enzyme gene DHPS1 29-30 lysine level 1.00E−139 Suh et al., unpublished Dihydrodipicolinate 308/336 (91%) synthase from rice (Oryza sativa) - key lysine biosynthetic enzyme FER 31-32 iron level 1.00E−139 Wu et al., unpublished Ferritin iron storage 251/255 (98%) protein from rice (Oryza sativa). FER1 33-34 iron level 1.00E−135 Wu et al., unpublished Ferritin iron storage 245/255 (96%) protein from rice (Oryza sativa). GAMYB1 35-36 enzyme activation 0 Gubler, F. et al. Plant Cell Myb transcription factor Physiol. 38(3): 362-365 from rice; barley ortholog (1997) mediates activation of 478/555 (86%) aleurone enzymes for mobilization of endoperm food stores for the developing embryo. GTMT 37-38 vitamin E level 1.00E−120 Shintani and DellaPenna, Arabidopsis thaliana Science 282(5396): 2098-2100 gamma-tocopherol (1998) methyltransferase, key 215/331 (64%) Vitamin E biosynthetic enzyme. Overexpression in Arabidopsis increases Vitamin E levels. ISPE 39-40 vitamin A level 1.00E−154 Lawrence et al., Plant Mol. 4-diphosphocytidyl-2-C- Biol. 33 (3), 483-492 (1997) methyl-D-erythritol kinase 258/336 (76%) from tomato (Lycopersicon esculentum) - key Vitamin A biosynthetic enzyme. OHP1 41-42 protein level 0 Nakase et al., Plant Mol. bZIP transcription factor Biol. 33 (3), 513-522 (1997) from rice (Oryza sativa); 423/425 (99%) positive regulator of seed storage protein genes.

[0420] Assays for testing for a variety of grain quality or nutritional composition qualities known to those skilled in the art are performed on transgenic plants and non-transgenic parental lines to determine alteration in any such qualities.

[0421] For example, but by no means limiting, such quality assays are performed essentially as described below.

[0422] An assay to analyze alterations in vitamin E content or beta-carotene (pro-vitamin A) content are performed essentially as described using high performance liquid chromatography (HPLC) in Fraser et al. Plant J. (2000) 24:551-458.

[0423] Assays for alteration of iron content are performed essentially as described in Goto et al. (1999) Nat. Biotech. 17:282-286 or Kamachi et al. (1992) Plant Physiol. 99:1481-1486.

[0424] Assays for alteration of enhanced phosphorus uptake are performed by growing plants under phosphorus limiting conditions for their entire life cycle, and growth (final dry mass) and yield (seed size and weight) are measured essentially as described in Fohse et al. (1988) Plant Soil 110:101-109.

[0425] Assays for alterantion of thiamin levels are performed essentially as described in Esteve et al. (2001) J. Agric. Food Chem. 49:1450.

[0426] The malting assays below are used for analyzing alterations due to the presence of GAMYB1. Malt and bacterial beta glucanase and cellulase assay procedure (azo barley glucan method) from Megazyme, Megazyme Int'l Ireland Ltd., Bray, co. Wicklow, Ireland, www.megazyme.com and the Amylazyme- alpha- amylase assay procedure from Megazyme.

[0427] A preferred assay for amino acid content of seeds is as follows:

[0428] Prepare: 80% EtOH in 45° C. water bath; 80% EtOH at room temp.; hexane; sealable glass tubes; 2M NH₄OH; 0.02M HCl; ddH₂O; and Dowex columns.

[0429] This protocol has been used for extraction of amino acids from seeds at 4DAF to mature. All samples are stored at −30° C. until extraction. Seeds are separated from the siliques and counted. Approximately 600 seeds are required for the each sample. This protocol is for extraction from approximately 600 seeds. Amino acids are quantified according to amount per 100 seeds (total amount), NOT amount per mg seeds (concentration). We believe this is a more accurate approach.

[0430] Crude Extract Preparation:

[0431] Homogenise approximately 600 seeds in 1 ml 45° C. 80% EtOH

[0432] 1. Split the sample into 2 eppendorf tubes

[0433] 2. Rinse the homogeniser 4 times with 300 μl of 45° C. 80% EtOH, transfering each rinse evenly into the 2 eppen tubes

[0434] 3. Centrifuge sample at 5,000 rpm for 10 min at 4° C.

[0435] 4. Transfer sup to fresh eppen tubes on ice

[0436] 5. Re-suspend pellets in 100 μl of 45° C. 80% EtOH (pellet wash)

[0437] 6. Vortex to re-suspend and place on shaker for 5 min

[0438] 7. Centrifuge sample at 5,000 rpm for 10 min at 4° C.

[0439] 8. Transfer sup to the eppen tubes on ice

[0440] 9. Supernatant fraction: Soluble amino acids fraction Pellet fraction: Protein-bound amino acids fraction

[0441] For the soluble amino acids fraction, go direct to Dowex Column Purification (step 23). For the protein-bound fraction, continue with Extraction of Protein-bound Amino Acids (step 12)

[0442] Extraction of Protein Bound Amino Acids

[0443] 12. Evaporate excess EtOH by putting sample on 45° C. heat block for 3 min

[0444] 13. Add 600 μl hexane and vortex on shaker for 30 min (in draft hood)

[0445] 14. Centrifuge sample at 5,000 rpm for 10 min at 4° C.

[0446] 15. Discard sup and resuspend pellet as much as possible in 1 ml 6M HCl

[0447] 16. Transfer the 2 solutions/sample into 1 sealable glass tube

[0448] 17. Seal the glass tube under vacuum and incubate at 110° C. for 18 hr to hydrolyze the protein

[0449] 18. After samples have cooled to rt, break open glass tube and transfer to eppen tubes

[0450] 19. Dry up samples in vacuum centrifuge (takes 3 to 4 hrs)

[0451] 20. Add 500 μl of 45° C. 80% EtOH. Vortex to resuspend and place on shaker for 5 min

[0452] 21. Centrifuge sample at 5,000 rpm for 10 min at 4° C.

[0453] Transfer sup to new eppen (solubilised protein-bound amino acids) and continue to Dowex Column Purification (step 23)

[0454] 23. Prepare 200 μl Dowex H⁺ column

[0455] 24. Flow through about 1 ml of rt 80% EtOH

[0456] 25. Apply sample in 4 stages, allowing to flow through by gravity

[0457] 26. Wash 3 times with 400 μl (2× column volume) of rt 80% EtOH (total=1.2 ml, 6× column volume)

[0458] 27. Wash 3 times with 400 μl (2× column volume) of ddH₂O (total1 .2 ml, 6× column volume)

[0459] 28. Elute sample into fresh eppen tubes over 4 stages with 250 μl of 2M NH₄OH (total=1.0 ml, 5× column volume)

[0460] 29. Keep samples on ice—samples can be stored o/n at 4° C. if desired

[0461] 30. Split the samples into 2 eppen tubes and dry sample in vacuum centrifuge with heater (approx. 2.5 hrs). Although sample can fit in 1 eppen, drying is quicker with the 2 smaller volumes

[0462] 31. Add 40 μl ice-cold 0.02M HCl to each eppen

[0463] 32. Vortex to re-suspend, place on a medium-speed shaker for 15 minutes

[0464] 33. Combine the samples into one of the eppen tubes then rinse the empty eppen with another 30 μl and add to the sample

[0465] 34. Transfer to millipore columns (yellow lid)

[0466] 35. Centrifuge for 1 min at 7,000 rpm at 4° C.

[0467] 36. Discard the filter column from the tube and seal with parafilm

[0468] 37. Store samples in 4° C., can be stored for up to 3 months

[0469] For the soluble amino acid fraction samples, use undiluted for HPLC analysis. The protein-bound samples may also need to be diluted

[0470] The millipore columns we use are Ultrafre-MC 0.22 μm filter units that resemble an eppendorf tube. The samples are analyzed by HPLC, preferably an M analyzer L8800 from Hitachi.

[0471] See references, Inaba, K., Fujiwara, T., Hayashi, H., Chino, M., Komeda, Y. and Naito, S. (1994). Isolation of an Arabidopsis thaliana mutant mto1 that overaccumulates soluble methionine: temporal and spatial patterns of soluble methionine accumulation. Plant Physiol. 10 104: 881-887, and Kho, C. and De Lumen, B. O. (1988). Identification and isolation of methionine-cysteine rich protein in soybean seed. Plant Food for Human Nutrition. 38: 287-296.

Example 7 Enhanced Yield Genes and Analysis

[0472] The function of the protein encoded by each yield related gene is determined from analysis of the open reading frame (ORF) in each cDNA as described in Example 1. Table 4 describes the assigned functions for these genes described in this application. TABLE 4 Enhanced Yield Genes SEQ ID Putative Function and Homology References Gene NO Similar Gene E value and % Homology FT 43-44 time to harvest 1.00E−197 Kardailsky et al., Science 286 Arabidopsis thaliana (5446), 1962-1965 (1999) flowering locus T (FT) 173/176 (98%) gene; mutation results in delay of flowering. IDS1 45-46 seed number 1.00E−66  Chuck et al., Genes Dev. 12 (8), IDS1 indeterminate 1145-1154 (1998) spikelet 1 from maize (Zea 135/214 (63%) mays) - regulator of floral  24/42 (57%) meristem determinacy IDS2 47-48 iron acquisition 1.00E−115 Mori and Nakanishi, unpublished Iron siderophore 204/344 (59%) biosynthetic enzyme gene IDS3 from barley (Hordeum vulgare); enhances iron uptake by roots. IDS3 49-50 iron acquisition 1.00E−120 Mori and Nakanishi, unpublished Iron siderophore 204/315 (64%) biosynthetic enzyme gene IDS3 from barley (Hordeum vulgare); enhances iron uptake by roots. IFL1 51-42 seed number 0 Zhong and Ye, Plant Cell 11 Arabidopsis thaliana (11), 2139-2152 (1999) homeodomain-leucine 576/840 (68%) zipper transcription factor IFL1 - positive regulator of inflorescence branching IRT1 53-54 iron acquisition 2.00E−97  Eckhardt et al., Plant Mol. Biol. Iron transporter 1 (IRT1) 45 (4), 437-448 (2001) from tomato (Lycopersicon 186/338 (55%) esculentum). NAAT 55-56 iron acquisition 1.00E−139 Takahashi et al., Plant Physiol. Nicotianamine 121 (3), 947-956 (1999) aminotransferase from 228/379 (60%) barley (Hordeum vulgare) iron siderophore biosynthetic enzyme gene; enhances iron uptake by roots. NAS1 57-58 iron acquisition 0 Higuchi et al., Plant J. 25 (2), Nicotianamine synthase 1 159-167 (2001) (NAS1) from rice (Oryza 331/332 (99%) sativa); iron siderophore biosynthetic enzyme gene; enhances iron uptake by roots. NRAMP1 59-60 iron acquisition 0 Belouchi et al., Plant Mol. Biol. Iron transporter Nramp1 29 (6), 1181-1196 (1995) from rice (Oryza sativa); 512/518 (98%) enhances iron uptake by roots. NRAMP2 61-62 iron acquisition 0 Belouchi et al., Plant Mol. Biol. Iron transporter from rice 33 (6), 1085-1092 (1997) (Oryza sativa); enhances 459/464 (98%) iron uptake by roots. PT1 63-64 phosphate acquisition 0 Kai and Adachi, unpublished Phospate transporter from 414/518 (79%) tobacco (Nicotiana tabacum); functions in uptake of phoshphate, a key plant nutrient, in roots.

[0473] There are a wide variety of methods for analyzing grain quality including, but not limited to, starch analysis, protein content and analysis, phosphate acquisition, and iron acquisition.

[0474] A preferred starch content assay is the Sigma Starch Assay Kit (Product no. STA-20; Sigma Chemical Co., St. Louis, Mo.). The protocol is available from the manufacturer.

[0475] A preferred protein content assay is the Biorad Bradford Assay Kit (#500-0002; Biorad, Hercules, Calif.).

[0476] The phosphate acquisition assay, is essentially performed by growing plants hydroponically under phosphate-limiting conditions (for example, 10 uM final concentration). Leaf phosphorus levels (Murphy and Riley (1962) Anal. Chim. Acta 27: 31-36) and growth (final dry weight and seed weight) are measured, comparing transgenic and non-transgenic plants.

[0477] Similarly, for the iron acquisition assay, plants are grown hydroponically under iron-limiting conditions, essentially as described in Thoiron et al. (1997) Plant Cell Env. 20:1051-1060. Assays include measurement of the extent of low iron-induced chlorosis (essentially as described in Takahashi et al. (2001) Nat. Biotech. 19: 466469) and growth measurements (final dry weight and seed weight), comparing transgenic and non-transgenic plants.

[0478] NIRS Assay

[0479] Near Infrared Reflectance Spectroscopy (NIRS) is used for evaluation of protein and amino acids in seeds by those in the art. Techniques are used to test individual grains or a sample of ground seeds as preferred or required. A number of NIRS assay techniques and devices are available to those in the art for analyzing a variety of samples, including grain quality.

[0480] NIRS calibrations for evaluation of a number of feed components (including protein) can be purchased on the open market and the best place to find what is available is probably the manufacturers of NIRS equipment. There are two main suppliers of NIRS-FOSS NIRS systems and Bran & Lubbe. There is also a group run by Pierre Dardenne at the University of Gembloux in Belgium who produce and sell calibrations.

[0481] Similarly, Perten Instruments, provides for all sorts of applications for NIR including measuring starch and protein. For altered protein composition, the highest resolution methods available currently are believed to be, for example, high performance capillary electrophoresis as described by George Lookhart in Journal of Chromatography A, 881 (2000) 23-36 and in Electrophoresis 2001, 1503-1509. There is a review in Current Opinion in Biotechnology 1999 on Production of modified polymeric carbohydrates 10,169-174, which is a good source of a range of methods.

[0482] The USDA intemet page, also has application notes with a list of methods to analyze grain quality listed under cultivar development, and the ARS News and Information section. And a general reference for the analysis of rice is by Barton et al., Agricultural Research, August 1998, pages 18-21.

[0483] The above-disclosed embodiments are illustrative. This disclosure of the invention will place one skilled in the art in possession of many variations of the invention. All such obvious and foreseeable variations are intended to be encompassed by the present invention. All references cited within are hereby incorporated by reference in their entirety.

1 64 1 1131 DNA Oryza sativa 1 atgctgacgg ataggtgggg agggaggagg gaggcgatgg agttcgggaa cggcgggtcc 60 tcctcgtcgg agcgcagggc ggcggcggag ggggcgacgc tggcgagaca gggttcggtg 120 tattcgctga cgttcgacga gttccagagc gcgctcgctg gtggcggcgg cggcggcggt 180 ggtggaagcg ggttcgggaa ggacttcggc tccatgaaca tggacgagct gctccggagc 240 atctggaccg cggaggagag ccaggccatg gcctccgcct ctggctccgc cgcgggggtg 300 ggcgtggccg tgggggcgcc gccgacgtcg ctgcagcgcc agggctcgct caccctgccc 360 cgcacgctca gcgccaagac ggtggacgag gtatggcgca accttgtgcg cgacgagcca 420 ccgccggtgg gggcggcgga tggcggcgat atgccacccc agcggcagtc gaccctcggg 480 gagatgaccc tggaggagtt cttggtcaga gccggcgtgg tccgagaaaa tccacccgct 540 gcgccgcccc ccgttccccc gccaatgccg ccgcggccag tcccggtggt ccccaagacc 600 actgccttct tgggaaactt ccccggtgcc aacgatgccg gcgcggcggc gctgggcttt 660 gcgccgctcg gcatggggga tccagccttg ggcaatggcc tgatgcccag ggcagtgcca 720 gtgggcttgc ctggcgccgc cgtcgctatg caaacagcgg tgaaccagtt tgattctggc 780 gataagggga acagcgacct gtcatcgccg acggagccaa tgccttattc cttcgaaggg 840 ttggtgaggg ggagaaggaa cggtggcgga gtagagaaag tggtggagag gaggcagagg 900 aggatgatca agaacaggga gtccgcggcg agatcccgcg cgcgcaagca ggcttacaca 960 ttggaattgg aagctgaagt tcagaaactc aaggagatga acaaggaatt ggagaggaaa 1020 caggcagata tcatggaaat gcagaaaaat gaggtagaag aaatgataaa ggatccattt 1080 ggaagaagga agagactttg cttgcgaaga acactgactg gtccctggtg a 1131 2 376 PRT Oryza sativa 2 Met Leu Thr Asp Arg Trp Gly Gly Arg Arg Glu Ala Met Glu Phe Gly 1 5 10 15 Asn Gly Gly Ser Ser Ser Ser Glu Arg Arg Ala Ala Ala Glu Gly Ala 20 25 30 Thr Leu Ala Arg Gln Gly Ser Val Tyr Ser Leu Thr Phe Asp Glu Phe 35 40 45 Gln Ser Ala Leu Ala Gly Gly Gly Gly Gly Gly Gly Gly Gly Ser Gly 50 55 60 Phe Gly Lys Asp Phe Gly Ser Met Asn Met Asp Glu Leu Leu Arg Ser 65 70 75 80 Ile Trp Thr Ala Glu Glu Ser Gln Ala Met Ala Ser Ala Ser Gly Ser 85 90 95 Ala Ala Gly Val Gly Val Ala Val Gly Ala Pro Pro Thr Ser Leu Gln 100 105 110 Arg Gln Gly Ser Leu Thr Leu Pro Arg Thr Leu Ser Ala Lys Thr Val 115 120 125 Asp Glu Val Trp Arg Asn Leu Val Arg Asp Glu Pro Pro Pro Val Gly 130 135 140 Ala Ala Asp Gly Gly Asp Met Pro Pro Gln Arg Gln Ser Thr Leu Gly 145 150 155 160 Glu Met Thr Leu Glu Glu Phe Leu Val Arg Ala Gly Val Val Arg Glu 165 170 175 Asn Pro Pro Ala Ala Pro Pro Pro Val Pro Pro Pro Met Pro Pro Arg 180 185 190 Pro Val Pro Val Val Pro Lys Thr Thr Ala Phe Leu Gly Asn Phe Pro 195 200 205 Gly Ala Asn Asp Ala Gly Ala Ala Ala Leu Gly Phe Ala Pro Leu Gly 210 215 220 Met Gly Asp Pro Ala Leu Gly Asn Gly Leu Met Pro Arg Ala Val Pro 225 230 235 240 Val Gly Leu Pro Gly Ala Ala Val Ala Met Gln Thr Ala Val Asn Gln 245 250 255 Phe Asp Ser Gly Asp Lys Gly Asn Ser Asp Leu Ser Ser Pro Thr Glu 260 265 270 Pro Met Pro Tyr Ser Phe Glu Gly Leu Val Arg Gly Arg Arg Asn Gly 275 280 285 Gly Gly Val Glu Lys Val Val Glu Arg Arg Gln Arg Arg Met Ile Lys 290 295 300 Asn Arg Glu Ser Ala Ala Arg Ser Arg Ala Arg Lys Gln Ala Tyr Thr 305 310 315 320 Leu Glu Leu Glu Ala Glu Val Gln Lys Leu Lys Glu Met Asn Lys Glu 325 330 335 Leu Glu Arg Lys Gln Ala Asp Ile Met Glu Met Gln Lys Asn Glu Val 340 345 350 Glu Glu Met Ile Lys Asp Pro Phe Gly Arg Arg Lys Arg Leu Cys Leu 355 360 365 Arg Arg Thr Leu Thr Gly Pro Trp 370 375 3 1113 DNA Oryza sativa 3 atggagaaat acgagccagt tcgggagatc ggggcgggca acttcggggt agcgaagctg 60 atgcggaaca aggagacgcg ggagctggtg gcgatgaagt tcatcgagag agggaacagg 120 atcgacgaga acgtgttccg ggagatcgtg aatcatcgtt cgctgcgtca cccgaacata 180 ataaggttca aggaggtggt ggtgacgggg aggcatctgg cgatcgtgat ggagtacgcg 240 gcgggagggg agctgttcga gaggatatgc gaggcgggga ggttccacga ggacgaggcg 300 cgctacttct tccagcagct ggtgtgcggg gtgagctact gccacgccat gcagatctgc 360 caccgcgacc tcaagctgga gaatacgctg ctggacggca gcccggcccc gcgcctcaag 420 atctgcgact tcggctactc caagtcctcc ctcctccact cccgccccaa atccaccgtc 480 ggcacccccg cctacatcgc ccccgaggtc ctctcccgcc gcgagtacga cggcaagctc 540 gccgacgtct ggtcctgcgg cgtcaccctc tacgtcatgc tcgtcggcgc ttaccctttc 600 gaggatccca aggaccccaa gaacttcaga aagaccatct cgcgcatcat gtccgtccag 660 tacaagatcc ccgagtacgt ccacgtctcc cagccctgcc gccacctcct ctcccgcatc 720 ttcgtcgcca acccctacaa gcgcatcagc atgggcgaga tcaagagcca cccctggttc 780 ctcaagaacc tgccgcgcga gctcaaggag gaggcgcagg ccgtctacta caaccgccgg 840 ggagccgatc acgcggcttc cagcgcaagt agtgcggctg ctgcagctgc cttctcgccg 900 cagagcgtgg aggacatcat gaggatcgtg caggaggcgc agaccgtccc caagcccgac 960 aagcccgtct ctggctacgg ctggggcacc gacgacgacg acgacgacca acaaccagct 1020 gaggaggagg acgaagaaga cgactacgac aggacggtgc gcgaggttca cgccagcgtc 1080 gacctcgaca tgtcaaacct ccaaatctcc tga 1113 4 370 PRT Oryza sativa 4 Met Glu Lys Tyr Glu Pro Val Arg Glu Ile Gly Ala Gly Asn Phe Gly 1 5 10 15 Val Ala Lys Leu Met Arg Asn Lys Glu Thr Arg Glu Leu Val Ala Met 20 25 30 Lys Phe Ile Glu Arg Gly Asn Arg Ile Asp Glu Asn Val Phe Arg Glu 35 40 45 Ile Val Asn His Arg Ser Leu Arg His Pro Asn Ile Ile Arg Phe Lys 50 55 60 Glu Val Val Val Thr Gly Arg His Leu Ala Ile Val Met Glu Tyr Ala 65 70 75 80 Ala Gly Gly Glu Leu Phe Glu Arg Ile Cys Glu Ala Gly Arg Phe His 85 90 95 Glu Asp Glu Ala Arg Tyr Phe Phe Gln Gln Leu Val Cys Gly Val Ser 100 105 110 Tyr Cys His Ala Met Gln Ile Cys His Arg Asp Leu Lys Leu Glu Asn 115 120 125 Thr Leu Leu Asp Gly Ser Pro Ala Pro Arg Leu Lys Ile Cys Asp Phe 130 135 140 Gly Tyr Ser Lys Ser Ser Leu Leu His Ser Arg Pro Lys Ser Thr Val 145 150 155 160 Gly Thr Pro Ala Tyr Ile Ala Pro Glu Val Leu Ser Arg Arg Glu Tyr 165 170 175 Asp Gly Lys Leu Ala Asp Val Trp Ser Cys Gly Val Thr Leu Tyr Val 180 185 190 Met Leu Val Gly Ala Tyr Pro Phe Glu Asp Pro Lys Asp Pro Lys Asn 195 200 205 Phe Arg Lys Thr Ile Ser Arg Ile Met Ser Val Gln Tyr Lys Ile Pro 210 215 220 Glu Tyr Val His Val Ser Gln Pro Cys Arg His Leu Leu Ser Arg Ile 225 230 235 240 Phe Val Ala Asn Pro Tyr Lys Arg Ile Ser Met Gly Glu Ile Lys Ser 245 250 255 His Pro Trp Phe Leu Lys Asn Leu Pro Arg Glu Leu Lys Glu Glu Ala 260 265 270 Gln Ala Val Tyr Tyr Asn Arg Arg Gly Ala Asp His Ala Ala Ser Ser 275 280 285 Ala Ser Ser Ala Ala Ala Ala Ala Ala Phe Ser Pro Gln Ser Val Glu 290 295 300 Asp Ile Met Arg Ile Val Gln Glu Ala Gln Thr Val Pro Lys Pro Asp 305 310 315 320 Lys Pro Val Ser Gly Tyr Gly Trp Gly Thr Asp Asp Asp Asp Asp Asp 325 330 335 Gln Gln Pro Ala Glu Glu Glu Asp Glu Glu Asp Asp Tyr Asp Arg Thr 340 345 350 Val Arg Glu Val His Ala Ser Val Asp Leu Asp Met Ser Asn Leu Gln 355 360 365 Ile Ser 370 5 1386 DNA Oryza sativa 5 atgccacaca gagcaggaga ggtgtcgtcg tcgtcttctc cggggagcat gtcgaaggcg 60 atgcagtgct tcgggttcgc cggctgggag agggatgagc ggcgtggccg gtcgtcggcg 120 gtggcctcgg cggcggcggc gacgacgcgt tcgctgtcgg cgcggtccaa cagcagcacg 180 tcgacggacc gcgacgcgcg gcggtcgggg tcggagtgct ccctgaacgt gtcgtcggag 240 atcagcgccg agtcgttcgg ccggtaccgg cagctgtcgc tgccgcagcg cgcgagcaac 300 aacctccgca tcttcacctt ccaggagctc aagagcgcca cccgcgggtt cagccgctcg 360 ctggtgctcg gcgagggcgg cttcggctgc gtctaccgcg gcaccatccg cagcgtcctc 420 gagcctcgcc ggagcgtcga ggtcgccatc aagcagctcg gccgcaaagg cctacagggg 480 cataaggagt gggtgacgga ggtgaacgtt cttggggtgg tggatcatcc gaacctggtg 540 aagctcatcg ggtactgcgc cgaggacgac gagaggggga tgcagctgct gctcgtctac 600 gagttcatgc ccaacgggag cctggcagat cacctgtcgt cgaggtcgcc gaggccggcg 660 tcgtgggcga tgcggctcag ggtggcgctc gacaccgcgc gcggcttgaa gtatctccat 720 gaagaatctg aaatcaagat aatatttcgt gatctgaagc cttccaacat tctgatcgac 780 gagaactgga acgcgaagct gtcagacttc ggattggcta gactggtatc tcaggatggc 840 agccatgtct ccactgcggt ggtgggaact attgggtatg cagctccaga gtacatccac 900 acagggcgcc tcagcagcaa gaacgacata tggagctacg gcgtggtgct ctacgaactc 960 cttaccggtc ggcgacctct ggacaggaac aggccgagag gcgaacagaa cctcatagag 1020 tgggtgaagc cctactccac tgactcaaag aagcttgaaa tcataatgga tccaaggctt 1080 gaagggagtt acagcttgaa gtcggcggcc aagctcgcct cggtggcaaa caagtgcctc 1140 gtgcgccacg ccaggcaccg gccaaagatg agcgaggtgc tggagatggt gcagaagatc 1200 gtcgatagca ctgacctcgg aacgccggag catcccctca tcagcaagtc aagagagctg 1260 acgcgtgatg agaagaaacg aaaagggctt gacctgaaga gaagatttgc tgatattaaa 1320 gctggagggg atcagagatg gtttacatgg cagagatgga gacccaaact tgtcagaaca 1380 caatga 1386 6 461 PRT Oryza sativa 6 Met Pro His Arg Ala Gly Glu Val Ser Ser Ser Ser Ser Pro Gly Ser 1 5 10 15 Met Ser Lys Ala Met Gln Cys Phe Gly Phe Ala Gly Trp Glu Arg Asp 20 25 30 Glu Arg Arg Gly Arg Ser Ser Ala Val Ala Ser Ala Ala Ala Ala Thr 35 40 45 Thr Arg Ser Leu Ser Ala Arg Ser Asn Ser Ser Thr Ser Thr Asp Arg 50 55 60 Asp Ala Arg Arg Ser Gly Ser Glu Cys Ser Leu Asn Val Ser Ser Glu 65 70 75 80 Ile Ser Ala Glu Ser Phe Gly Arg Tyr Arg Gln Leu Ser Leu Pro Gln 85 90 95 Arg Ala Ser Asn Asn Leu Arg Ile Phe Thr Phe Gln Glu Leu Lys Ser 100 105 110 Ala Thr Arg Gly Phe Ser Arg Ser Leu Val Leu Gly Glu Gly Gly Phe 115 120 125 Gly Cys Val Tyr Arg Gly Thr Ile Arg Ser Val Leu Glu Pro Arg Arg 130 135 140 Ser Val Glu Val Ala Ile Lys Gln Leu Gly Arg Lys Gly Leu Gln Gly 145 150 155 160 His Lys Glu Trp Val Thr Glu Val Asn Val Leu Gly Val Val Asp His 165 170 175 Pro Asn Leu Val Lys Leu Ile Gly Tyr Cys Ala Glu Asp Asp Glu Arg 180 185 190 Gly Met Gln Leu Leu Leu Val Tyr Glu Phe Met Pro Asn Gly Ser Leu 195 200 205 Ala Asp His Leu Ser Ser Arg Ser Pro Arg Pro Ala Ser Trp Ala Met 210 215 220 Arg Leu Arg Val Ala Leu Asp Thr Ala Arg Gly Leu Lys Tyr Leu His 225 230 235 240 Glu Glu Ser Glu Ile Lys Ile Ile Phe Arg Asp Leu Lys Pro Ser Asn 245 250 255 Ile Leu Ile Asp Glu Asn Trp Asn Ala Lys Leu Ser Asp Phe Gly Leu 260 265 270 Ala Arg Leu Val Ser Gln Asp Gly Ser His Val Ser Thr Ala Val Val 275 280 285 Gly Thr Ile Gly Tyr Ala Ala Pro Glu Tyr Ile His Thr Gly Arg Leu 290 295 300 Ser Ser Lys Asn Asp Ile Trp Ser Tyr Gly Val Val Leu Tyr Glu Leu 305 310 315 320 Leu Thr Gly Arg Arg Pro Leu Asp Arg Asn Arg Pro Arg Gly Glu Gln 325 330 335 Asn Leu Ile Glu Trp Val Lys Pro Tyr Ser Thr Asp Ser Lys Lys Leu 340 345 350 Glu Ile Ile Met Asp Pro Arg Leu Glu Gly Ser Tyr Ser Leu Lys Ser 355 360 365 Ala Ala Lys Leu Ala Ser Val Ala Asn Lys Cys Leu Val Arg His Ala 370 375 380 Arg His Arg Pro Lys Met Ser Glu Val Leu Glu Met Val Gln Lys Ile 385 390 395 400 Val Asp Ser Thr Asp Leu Gly Thr Pro Glu His Pro Leu Ile Ser Lys 405 410 415 Ser Arg Glu Leu Thr Arg Asp Glu Lys Lys Arg Lys Gly Leu Asp Leu 420 425 430 Lys Arg Arg Phe Ala Asp Ile Lys Ala Gly Gly Asp Gln Arg Trp Phe 435 440 445 Thr Trp Gln Arg Trp Arg Pro Lys Leu Val Arg Thr Gln 450 455 460 7 1242 DNA Oryza sativa 7 atggcccggc tgctactctc cggcgtcgcg ccgctccccc tcctcccctg ccgccgtcgc 60 gccattgcat ttgcgctccc acttgggaat gtccgcctcc gcctccgtgt ggccgcaccc 120 accagccgcg tggccaccgt ggaggaggac gacaatgaaa ataatgctcc tcctcctcct 180 tgtgaggact tcgacccggg cgcggcgccc ccgtttggtc tggccgacat ccgcgccgct 240 atccccaagc actgttgggt gaaggacccc tggcgatcca tggggtacgt gctgcgcgac 300 gtggtggtgg tgttcgccct cgctgccgcc gccgcgcgcc tccacagctg cctcgcctgg 360 ccgctctact gggcggcgca gggaaccatg ttctgggcgc tcttcgtcct cggccacgac 420 tgcgggcacg ggagcttctc caacaactcg aggctcaaca gcgtgatggg ccacatactc 480 cactcctcca tcctcgtacc ctaccatggc tggaggatta gccacaggac gcatcatcag 540 aaccatggcc atgtcgacaa ggatgagtcc tggcatcccc tccccgagcg gctgtacagg 600 agccttaaca gagccacccg gatgctccgc ttctccatac ccttccccat gctcgcctac 660 ccattctacc tgtggtctcg gagcccagga aagtctggtt cgcatttcca tcccagcagc 720 gacctgttcc agcccaacga aaggaacgat gtgctgacat ccacagcgtg ctgggtggcc 780 atggctgccc tcctcgcagg cctcaccttc ctcatgggac ccctcctcat gctcaacctc 840 tactttgtcc cttactggat ttttgttatg tggctggact tcgtcaccta cttgcaccat 900 cacggccaca acgacaagct gccctggtac cgtggcaagg aatggagcta tttgcgggga 960 ggactgacga cagtggacag ggactatggg tggatcaaca acatccacca cgacatcggg 1020 acacatgtca ttcaccatct tttcccccaa atcccgcatt accatctaat tgaggcgacg 1080 gaagcagcaa agggtgtgat ggggaaatac tacagggagc cggacaagtc tgggcctttt 1140 cccttacacc tgtttggagc gctgtcccgg agcttgaaac gcgaccacta tgtcagcgac 1200 accggagatg tggtctacta ccagaccgac cctgctaact aa 1242 8 413 PRT Oryza sativa 8 Met Ala Arg Leu Leu Leu Ser Gly Val Ala Pro Leu Pro Leu Leu Pro 1 5 10 15 Cys Arg Arg Arg Ala Ile Ala Phe Ala Leu Pro Leu Gly Asn Val Arg 20 25 30 Leu Arg Leu Arg Val Ala Ala Pro Thr Ser Arg Val Ala Thr Val Glu 35 40 45 Glu Asp Asp Asn Glu Asn Asn Ala Pro Pro Pro Pro Cys Glu Asp Phe 50 55 60 Asp Pro Gly Ala Ala Pro Pro Phe Gly Leu Ala Asp Ile Arg Ala Ala 65 70 75 80 Ile Pro Lys His Cys Trp Val Lys Asp Pro Trp Arg Ser Met Gly Tyr 85 90 95 Val Leu Arg Asp Val Val Val Val Phe Ala Leu Ala Ala Ala Ala Ala 100 105 110 Arg Leu His Ser Cys Leu Ala Trp Pro Leu Tyr Trp Ala Ala Gln Gly 115 120 125 Thr Met Phe Trp Ala Leu Phe Val Leu Gly His Asp Cys Gly His Gly 130 135 140 Ser Phe Ser Asn Asn Ser Arg Leu Asn Ser Val Met Gly His Ile Leu 145 150 155 160 His Ser Ser Ile Leu Val Pro Tyr His Gly Trp Arg Ile Ser His Arg 165 170 175 Thr His His Gln Asn His Gly His Val Asp Lys Asp Glu Ser Trp His 180 185 190 Pro Leu Pro Glu Arg Leu Tyr Arg Ser Leu Asn Arg Ala Thr Arg Met 195 200 205 Leu Arg Phe Ser Ile Pro Phe Pro Met Leu Ala Tyr Pro Phe Tyr Leu 210 215 220 Trp Ser Arg Ser Pro Gly Lys Ser Gly Ser His Phe His Pro Ser Ser 225 230 235 240 Asp Leu Phe Gln Pro Asn Glu Arg Asn Asp Val Leu Thr Ser Thr Ala 245 250 255 Cys Trp Val Ala Met Ala Ala Leu Leu Ala Gly Leu Thr Phe Leu Met 260 265 270 Gly Pro Leu Leu Met Leu Asn Leu Tyr Phe Val Pro Tyr Trp Ile Phe 275 280 285 Val Met Trp Leu Asp Phe Val Thr Tyr Leu His His His Gly His Asn 290 295 300 Asp Lys Leu Pro Trp Tyr Arg Gly Lys Glu Trp Ser Tyr Leu Arg Gly 305 310 315 320 Gly Leu Thr Thr Val Asp Arg Asp Tyr Gly Trp Ile Asn Asn Ile His 325 330 335 His Asp Ile Gly Thr His Val Ile His His Leu Phe Pro Gln Ile Pro 340 345 350 His Tyr His Leu Ile Glu Ala Thr Glu Ala Ala Lys Gly Val Met Gly 355 360 365 Lys Tyr Tyr Arg Glu Pro Asp Lys Ser Gly Pro Phe Pro Leu His Leu 370 375 380 Phe Gly Ala Leu Ser Arg Ser Leu Lys Arg Asp His Tyr Val Ser Asp 385 390 395 400 Thr Gly Asp Val Val Tyr Tyr Gln Thr Asp Pro Ala Asn 405 410 9 1077 DNA Oryza sativa 9 atgtcgcagg ccgccgggaa cccctacgcc gctgagctcg ccgccgccaa gaaggccgtc 60 accctcgccg cccgcctctg ccaggcggtg caaaaggaca ttctgcagtc tggtgttcag 120 tctaaggcgg atcaaagtcc ggtgacagtt gccgattatg ggtctcaaat attggtaagc 180 cttgtcttga aaatggaagc accagcttct tcttccttct ctatggtggc tgaggaggac 240 tcggaagaat tgaggaaaga aggcgcagaa gaaattttag aaaatatcac cgagctcgta 300 aacgaaacta tcgtagatga tggtacatac agcatttact tctctaagga aggtatcctc 360 tctgcaattg acgatggcaa gtctgaggga ggtccatctg ggcgacactg ggtgctagat 420 ccaattgatg ggactaaagg tttcttaagg ggagaccaat atgctattgc cctggctctg 480 cttgatgagg gtaaagttgt tttgggtgta ttggcttgtc ccaacctttc tttgggatca 540 ataggcaacc ttaatggtgg ctcctcggga gatcaagttg gtgctctctt ttctgctact 600 attggttgtg gagctgaagt agagtcttta cagggctctc cagcacaaaa gattagtgtc 660 tgttccatcg acaatccagt cgaagcttca ttctttgagt cctacgaagg ggcacactcc 720 ttgcgtgatt taacaggctc cattgcggag aaacttggtg tccaagctcc tccagttaga 780 attgatagcc aagcaaaata cggtgcccta gcccgaggtg acggtgccat ttacttgcgt 840 tttccacaca aaggttacag agagaagatc tgggatcatg cagctgggtc aatcgtcgtg 900 acagaagctg gaggtctggt gacagatgca tcaggaaacg atttggattt ctccaaaggg 960 agatttcttg atctcgacac agggatcatc gcgacgaaca agcagctgat gccttcactc 1020 ctgaaggctg tgcaagatgc catcaaggag caaaaccagg ctgcttcccc gttgtag 1077 10 358 PRT Oryza sativa 10 Met Ser Gln Ala Ala Gly Asn Pro Tyr Ala Ala Glu Leu Ala Ala Ala 1 5 10 15 Lys Lys Ala Val Thr Leu Ala Ala Arg Leu Cys Gln Ala Val Gln Lys 20 25 30 Asp Ile Leu Gln Ser Gly Val Gln Ser Lys Ala Asp Gln Ser Pro Val 35 40 45 Thr Val Ala Asp Tyr Gly Ser Gln Ile Leu Val Ser Leu Val Leu Lys 50 55 60 Met Glu Ala Pro Ala Ser Ser Ser Phe Ser Met Val Ala Glu Glu Asp 65 70 75 80 Ser Glu Glu Leu Arg Lys Glu Gly Ala Glu Glu Ile Leu Glu Asn Ile 85 90 95 Thr Glu Leu Val Asn Glu Thr Ile Val Asp Asp Gly Thr Tyr Ser Ile 100 105 110 Tyr Phe Ser Lys Glu Gly Ile Leu Ser Ala Ile Asp Asp Gly Lys Ser 115 120 125 Glu Gly Gly Pro Ser Gly Arg His Trp Val Leu Asp Pro Ile Asp Gly 130 135 140 Thr Lys Gly Phe Leu Arg Gly Asp Gln Tyr Ala Ile Ala Leu Ala Leu 145 150 155 160 Leu Asp Glu Gly Lys Val Val Leu Gly Val Leu Ala Cys Pro Asn Leu 165 170 175 Ser Leu Gly Ser Ile Gly Asn Leu Asn Gly Gly Ser Ser Gly Asp Gln 180 185 190 Val Gly Ala Leu Phe Ser Ala Thr Ile Gly Cys Gly Ala Glu Val Glu 195 200 205 Ser Leu Gln Gly Ser Pro Ala Gln Lys Ile Ser Val Cys Ser Ile Asp 210 215 220 Asn Pro Val Glu Ala Ser Phe Phe Glu Ser Tyr Glu Gly Ala His Ser 225 230 235 240 Leu Arg Asp Leu Thr Gly Ser Ile Ala Glu Lys Leu Gly Val Gln Ala 245 250 255 Pro Pro Val Arg Ile Asp Ser Gln Ala Lys Tyr Gly Ala Leu Ala Arg 260 265 270 Gly Asp Gly Ala Ile Tyr Leu Arg Phe Pro His Lys Gly Tyr Arg Glu 275 280 285 Lys Ile Trp Asp His Ala Ala Gly Ser Ile Val Val Thr Glu Ala Gly 290 295 300 Gly Leu Val Thr Asp Ala Ser Gly Asn Asp Leu Asp Phe Ser Lys Gly 305 310 315 320 Arg Phe Leu Asp Leu Asp Thr Gly Ile Ile Ala Thr Asn Lys Gln Leu 325 330 335 Met Pro Ser Leu Leu Lys Ala Val Gln Asp Ala Ile Lys Glu Gln Asn 340 345 350 Gln Ala Ala Ser Pro Leu 355 11 1257 DNA Oryza sativa 11 atgccgcccg ggccgttcgt ggcgcgcgac ccgcgggtgg tggcgctgct cgacgccgcc 60 tccttccccg tcctgttcga cacgtcgctc gtcgacaaga ccgacctctt caccggcacc 120 ttcatgccgt ccaccgacct caccggcggg taccgcgtcc tctcctacct tgacccctcc 180 gagcccaacc acgcgccgct caagaccctc ctcttctacc tcctctccca ccggcggcag 240 caggtgatcc ccaagttccg cgaggtgtac ggcgacctgt tcggcctcat ggagaacgac 300 ctcgcccgcg tcggcaaggc cgacttcggc gtccacaacg acgccgccgc gttcggcttc 360 ctctgccagg ggctcctcgg ccgcgacccg gccaagtcgg cgctggggcg cgacgggccc 420 aagctgatca ccaagtgggt gctgttccag ctcagcccgc tgctcagcct cggcctcccc 480 accctcgtcg aggacacgct cctccactcg ctccgcctcc cgccggcgct ggtgaagaag 540 gactacgacc gcctcgccga cttcttccgg gacgcggcca aggccgtcgt cgacgagggg 600 gagcgcctcg gcattgcacg ggaggaggcc gtgcacaaca tcctcttcgc gctctgcttc 660 aactcgttcg gcgggatgaa gatcctgttc ccgacgctgg tgaagtggct gggccgcgcc 720 ggggcgcgtg tgcacgggcg gctcgccacc gaggtgcgcg gcgccgtgcg ggacaacggc 780 ggggaggtga cgatgaaggc gctggcggag atgccgctgg tgaagtcggc ggtgtacgag 840 gcgctgcgga tcgagccgcc ggtggcgatg cagtacggga gggcgaagcg ggacatggtg 900 gtggagagcc acgactacgg gtacgaggtg agggaagggg agatgctgtt cgggtaccag 960 cccatggcga ccaaggaccc gcgggtgttc gcgcggccgg aggagtacgt gccggacagg 1020 ttcctcggcg aggacggcgc gcggctgctc cgccacgtcg tgtggtccaa cgggcccgag 1080 acggcggcgc ccaccctgca cgacaagcag tgcgccggca aggacttcgt cgtgctcgtc 1140 gcgcgcctcc tcctcgtcga gctcttcctc cgatacgact ccttcgacgt cgaggtcggc 1200 acctccacgc tcggctcatc tgtcaccgtc acctcgctca agaaggccac cttctga 1257 12 418 PRT Oryza sativa 12 Met Pro Pro Gly Pro Phe Val Ala Arg Asp Pro Arg Val Val Ala Leu 1 5 10 15 Leu Asp Ala Ala Ser Phe Pro Val Leu Phe Asp Thr Ser Leu Val Asp 20 25 30 Lys Thr Asp Leu Phe Thr Gly Thr Phe Met Pro Ser Thr Asp Leu Thr 35 40 45 Gly Gly Tyr Arg Val Leu Ser Tyr Leu Asp Pro Ser Glu Pro Asn His 50 55 60 Ala Pro Leu Lys Thr Leu Leu Phe Tyr Leu Leu Ser His Arg Arg Gln 65 70 75 80 Gln Val Ile Pro Lys Phe Arg Glu Val Tyr Gly Asp Leu Phe Gly Leu 85 90 95 Met Glu Asn Asp Leu Ala Arg Val Gly Lys Ala Asp Phe Gly Val His 100 105 110 Asn Asp Ala Ala Ala Phe Gly Phe Leu Cys Gln Gly Leu Leu Gly Arg 115 120 125 Asp Pro Ala Lys Ser Ala Leu Gly Arg Asp Gly Pro Lys Leu Ile Thr 130 135 140 Lys Trp Val Leu Phe Gln Leu Ser Pro Leu Leu Ser Leu Gly Leu Pro 145 150 155 160 Thr Leu Val Glu Asp Thr Leu Leu His Ser Leu Arg Leu Pro Pro Ala 165 170 175 Leu Val Lys Lys Asp Tyr Asp Arg Leu Ala Asp Phe Phe Arg Asp Ala 180 185 190 Ala Lys Ala Val Val Asp Glu Gly Glu Arg Leu Gly Ile Ala Arg Glu 195 200 205 Glu Ala Val His Asn Ile Leu Phe Ala Leu Cys Phe Asn Ser Phe Gly 210 215 220 Gly Met Lys Ile Leu Phe Pro Thr Leu Val Lys Trp Leu Gly Arg Ala 225 230 235 240 Gly Ala Arg Val His Gly Arg Leu Ala Thr Glu Val Arg Gly Ala Val 245 250 255 Arg Asp Asn Gly Gly Glu Val Thr Met Lys Ala Leu Ala Glu Met Pro 260 265 270 Leu Val Lys Ser Ala Val Tyr Glu Ala Leu Arg Ile Glu Pro Pro Val 275 280 285 Ala Met Gln Tyr Gly Arg Ala Lys Arg Asp Met Val Val Glu Ser His 290 295 300 Asp Tyr Gly Tyr Glu Val Arg Glu Gly Glu Met Leu Phe Gly Tyr Gln 305 310 315 320 Pro Met Ala Thr Lys Asp Pro Arg Val Phe Ala Arg Pro Glu Glu Tyr 325 330 335 Val Pro Asp Arg Phe Leu Gly Glu Asp Gly Ala Arg Leu Leu Arg His 340 345 350 Val Val Trp Ser Asn Gly Pro Glu Thr Ala Ala Pro Thr Leu His Asp 355 360 365 Lys Gln Cys Ala Gly Lys Asp Phe Val Val Leu Val Ala Arg Leu Leu 370 375 380 Leu Val Glu Leu Phe Leu Arg Tyr Asp Ser Phe Asp Val Glu Val Gly 385 390 395 400 Thr Ser Thr Leu Gly Ser Ser Val Thr Val Thr Ser Leu Lys Lys Ala 405 410 415 Thr Phe 13 1521 DNA Oryza sativa 13 atggagttct tcactgagta tggagaagca agccagtacc agatccagga agtcattggc 60 aaaggaagtt atggagtagt tgctgctgca gtagataccc gcacgggtga gcgggttgca 120 atcaagaaga tcaatgatgt gtttgagcat gtatcagacg ctacgcgcat attgcgtgag 180 atcaagctcc ttcgtctgct ccgtcaccca gacatagttg agatcaaaca cattatgctt 240 cccccttctc gaagggagtt ccaagatatt tatgttgttt ttgagctcat ggaatcagat 300 ctccatcaag tcatcagagc gaacgatgac ctcaccccgg agcactacca gtttttcctg 360 taccaacttc tccgtgctct caagtacatc catgcagcta atgtatttca tcgcgatcta 420 aagcccaaga atatactggc aaactcagac tgcaaattga aaatatgtga tttcggactt 480 gcccgagcat cattcaatga tgccccttca gcaatatttt ggacggatta tgttgcaacg 540 aggtggtacc gagcacctga attatgtggc tcatttttct ccaaatacac tcctgcaatt 600 gatatttgga gtattgggtg catatttgct gaacttctca ctgggagacc actatttcct 660 gggaagaatg ttgtgcacca attagatatt ataacagatc ttcttggaac tccatcatca 720 gaaaccttat ccaggattcg aaatgagaag gccaggagat acttgagcac catgcagaaa 780 aaacatgctg tccccttctc tcagaagttc cgcaatactg accccttggc tcttcgtctg 840 ctagagcgtt tactggcatt tgatcctaaa gatcggtctt cagctgaaga agctttggct 900 gatccgtact tcgcaagtct tgctaatgtg gaacgtgagc cctcaagaca tccaatctca 960 aaacttgagt ttgaattcga gagacggaag ctgacaaaag atgatgttag agaattaatt 1020 tatcgagaga ttttggagta tcacccacag atgctgcaag agtatatgaa aggtggagag 1080 cagattagct tcctctatcc aagtggggtt gatcgcttca aacgacagtt tgcacacctt 1140 gaggagaact acagcaaagg agaaagaggt tctccactgc agaggaagca tgcttcttta 1200 ccgagggaga gagtaggtgt atcaaaggat ggttataacc aacaaaacac caatgaccaa 1260 gagaggagtg cagattccgt tgcccgcact acagtaagcc ctccaatgtc acaagatgca 1320 caacaacatg gatctgctgg ccaaaatggt gtgacatcca cagacttgag ttcgaggagc 1380 tatctgaaga gtgcaagcat tagtgcttcc aagtgtgtcg ctgtcaagga caataaagaa 1440 ccagaggatg attacatctc tgaagaaatg gaagggtcgg tcgatggatt gtctgaacaa 1500 gtctccagga tgcactccta g 1521 14 506 PRT Oryza sativa 14 Met Glu Phe Phe Thr Glu Tyr Gly Glu Ala Ser Gln Tyr Gln Ile Gln 1 5 10 15 Glu Val Ile Gly Lys Gly Ser Tyr Gly Val Val Ala Ala Ala Val Asp 20 25 30 Thr Arg Thr Gly Glu Arg Val Ala Ile Lys Lys Ile Asn Asp Val Phe 35 40 45 Glu His Val Ser Asp Ala Thr Arg Ile Leu Arg Glu Ile Lys Leu Leu 50 55 60 Arg Leu Leu Arg His Pro Asp Ile Val Glu Ile Lys His Ile Met Leu 65 70 75 80 Pro Pro Ser Arg Arg Glu Phe Gln Asp Ile Tyr Val Val Phe Glu Leu 85 90 95 Met Glu Ser Asp Leu His Gln Val Ile Arg Ala Asn Asp Asp Leu Thr 100 105 110 Pro Glu His Tyr Gln Phe Phe Leu Tyr Gln Leu Leu Arg Ala Leu Lys 115 120 125 Tyr Ile His Ala Ala Asn Val Phe His Arg Asp Leu Lys Pro Lys Asn 130 135 140 Ile Leu Ala Asn Ser Asp Cys Lys Leu Lys Ile Cys Asp Phe Gly Leu 145 150 155 160 Ala Arg Ala Ser Phe Asn Asp Ala Pro Ser Ala Ile Phe Trp Thr Asp 165 170 175 Tyr Val Ala Thr Arg Trp Tyr Arg Ala Pro Glu Leu Cys Gly Ser Phe 180 185 190 Phe Ser Lys Tyr Thr Pro Ala Ile Asp Ile Trp Ser Ile Gly Cys Ile 195 200 205 Phe Ala Glu Leu Leu Thr Gly Arg Pro Leu Phe Pro Gly Lys Asn Val 210 215 220 Val His Gln Leu Asp Ile Ile Thr Asp Leu Leu Gly Thr Pro Ser Ser 225 230 235 240 Glu Thr Leu Ser Arg Ile Arg Asn Glu Lys Ala Arg Arg Tyr Leu Ser 245 250 255 Thr Met Gln Lys Lys His Ala Val Pro Phe Ser Gln Lys Phe Arg Asn 260 265 270 Thr Asp Pro Leu Ala Leu Arg Leu Leu Glu Arg Leu Leu Ala Phe Asp 275 280 285 Pro Lys Asp Arg Ser Ser Ala Glu Glu Ala Leu Ala Asp Pro Tyr Phe 290 295 300 Ala Ser Leu Ala Asn Val Glu Arg Glu Pro Ser Arg His Pro Ile Ser 305 310 315 320 Lys Leu Glu Phe Glu Phe Glu Arg Arg Lys Leu Thr Lys Asp Asp Val 325 330 335 Arg Glu Leu Ile Tyr Arg Glu Ile Leu Glu Tyr His Pro Gln Met Leu 340 345 350 Gln Glu Tyr Met Lys Gly Gly Glu Gln Ile Ser Phe Leu Tyr Pro Ser 355 360 365 Gly Val Asp Arg Phe Lys Arg Gln Phe Ala His Leu Glu Glu Asn Tyr 370 375 380 Ser Lys Gly Glu Arg Gly Ser Pro Leu Gln Arg Lys His Ala Ser Leu 385 390 395 400 Pro Arg Glu Arg Val Gly Val Ser Lys Asp Gly Tyr Asn Gln Gln Asn 405 410 415 Thr Asn Asp Gln Glu Arg Ser Ala Asp Ser Val Ala Arg Thr Thr Val 420 425 430 Ser Pro Pro Met Ser Gln Asp Ala Gln Gln His Gly Ser Ala Gly Gln 435 440 445 Asn Gly Val Thr Ser Thr Asp Leu Ser Ser Arg Ser Tyr Leu Lys Ser 450 455 460 Ala Ser Ile Ser Ala Ser Lys Cys Val Ala Val Lys Asp Asn Lys Glu 465 470 475 480 Pro Glu Asp Asp Tyr Ile Ser Glu Glu Met Glu Gly Ser Val Asp Gly 485 490 495 Leu Ser Glu Gln Val Ser Arg Met His Ser 500 505 15 1185 DNA Oryza sativa 15 atggatcggc cgccgccgga tcagcagcgg cagaagcagg cgccgctctt ctcgccgtac 60 cagatgcccc gcttccgcct caaccaccgg gtggtgctgg cgccgatgac gcggtgcagg 120 gcgatcggcg gggtgcccgg cccggcgctg gcggagtact acgcgcagcg gaccacccag 180 ggtggcctgc tcatctccga gggcaccgtc gtctcgcccg ctggcccggg gtttcctcat 240 gtccctggga tatacaatca agagcagact gatgcatgga agaaggtggt ggatgctgtt 300 catgccaagg gaggcatctt tttctgccag ttatggcatg taggcagagc ttctcaccaa 360 gtataccagc caaacggtgc tgcaccaata tcctcaactg ataagccaat atcagcaaga 420 tggagaatac tgatgcctga tggctcctat ggcaagtatc ctaaacctag gcgcctggca 480 gcatcggaaa tacctgaaat tgtcgaacaa tatcgtcaag ccgccattaa tgccattgaa 540 gcaggttttg atggcattga gatccatggt gctcatggct atatcattga tcaattccta 600 aaggatggaa tcaatgaccg cactgacgag tatggtggct cactttccaa ccgctgccgg 660 ttcctacttg aggtaactag ggctgtggtt tctgccattg gagcagaccg agtcgcggtg 720 aggatatcac cagccattga tcaccttgac gcctatgatt cagaccccat taagctcggc 780 atggccgttg ttgagcggct gaatgctctc cagcagcagt cagggcggct cgcctacctc 840 cacgtcacgc agccacggta caccgcctac gggcagaccg agtctgggca gcatggcagt 900 gccgaggagg agagccgcct gatgcgcacc ctccggggca cgtaccaggg cacattcatg 960 tgcagtggcg gctacacgcg ggagcttggg ttggaagcag tggagagcgg cgatgccgac 1020 ctggtgtcgt acgggcggct cttcatatca aacccggacc tggtcgagcg gttcaggctg 1080 aacgccgggc tgaacaagta cgtgcgtaag acattctaca cgcccgatcc tgtcgtgggt 1140 tacacggact atccgttcct cggacagcct aagtcgcgga tgtaa 1185 16 394 PRT Oryza sativa 16 Met Asp Arg Pro Pro Pro Asp Gln Gln Arg Gln Lys Gln Ala Pro Leu 1 5 10 15 Phe Ser Pro Tyr Gln Met Pro Arg Phe Arg Leu Asn His Arg Val Val 20 25 30 Leu Ala Pro Met Thr Arg Cys Arg Ala Ile Gly Gly Val Pro Gly Pro 35 40 45 Ala Leu Ala Glu Tyr Tyr Ala Gln Arg Thr Thr Gln Gly Gly Leu Leu 50 55 60 Ile Ser Glu Gly Thr Val Val Ser Pro Ala Gly Pro Gly Phe Pro His 65 70 75 80 Val Pro Gly Ile Tyr Asn Gln Glu Gln Thr Asp Ala Trp Lys Lys Val 85 90 95 Val Asp Ala Val His Ala Lys Gly Gly Ile Phe Phe Cys Gln Leu Trp 100 105 110 His Val Gly Arg Ala Ser His Gln Val Tyr Gln Pro Asn Gly Ala Ala 115 120 125 Pro Ile Ser Ser Thr Asp Lys Pro Ile Ser Ala Arg Trp Arg Ile Leu 130 135 140 Met Pro Asp Gly Ser Tyr Gly Lys Tyr Pro Lys Pro Arg Arg Leu Ala 145 150 155 160 Ala Ser Glu Ile Pro Glu Ile Val Glu Gln Tyr Arg Gln Ala Ala Ile 165 170 175 Asn Ala Ile Glu Ala Gly Phe Asp Gly Ile Glu Ile His Gly Ala His 180 185 190 Gly Tyr Ile Ile Asp Gln Phe Leu Lys Asp Gly Ile Asn Asp Arg Thr 195 200 205 Asp Glu Tyr Gly Gly Ser Leu Ser Asn Arg Cys Arg Phe Leu Leu Glu 210 215 220 Val Thr Arg Ala Val Val Ser Ala Ile Gly Ala Asp Arg Val Ala Val 225 230 235 240 Arg Ile Ser Pro Ala Ile Asp His Leu Asp Ala Tyr Asp Ser Asp Pro 245 250 255 Ile Lys Leu Gly Met Ala Val Val Glu Arg Leu Asn Ala Leu Gln Gln 260 265 270 Gln Ser Gly Arg Leu Ala Tyr Leu His Val Thr Gln Pro Arg Tyr Thr 275 280 285 Ala Tyr Gly Gln Thr Glu Ser Gly Gln His Gly Ser Ala Glu Glu Glu 290 295 300 Ser Arg Leu Met Arg Thr Leu Arg Gly Thr Tyr Gln Gly Thr Phe Met 305 310 315 320 Cys Ser Gly Gly Tyr Thr Arg Glu Leu Gly Leu Glu Ala Val Glu Ser 325 330 335 Gly Asp Ala Asp Leu Val Ser Tyr Gly Arg Leu Phe Ile Ser Asn Pro 340 345 350 Asp Leu Val Glu Arg Phe Arg Leu Asn Ala Gly Leu Asn Lys Tyr Val 355 360 365 Arg Lys Thr Phe Tyr Thr Pro Asp Pro Val Val Gly Tyr Thr Asp Tyr 370 375 380 Pro Phe Leu Gly Gln Pro Lys Ser Arg Met 385 390 17 678 DNA Oryza sativa 17 atgcattgct gcatgtcgct tcatcctcac cgccgccacg gcgacggcga cgtcgacgga 60 tcagcatcag gatcaggatc agcgcgcctc accgccggcc tcatcaactt cctcgaatcg 120 cgtcgcgccg gcgccatgag caccaccaac agctcatcct ctgtctctgt cccagccatg 180 gacgcccatg gacaggagga ggaggaggag ccgatgcagg tgcagcaaca gcaggcgttc 240 cgcggggtgc gcaagcggcc atggggcaag tttgcggcgg agatccgcga ctcgacgcgc 300 aacggcgtgc gcgtgtggct gggcacgttc gacagcgcgg aggaggcggc gctggcctac 360 gaccaggcgg cgttcgccat gcgcgggtcg gcggcggtgc tcaacttccc catggagcag 420 gtgaggcgtt ccatggacat gtccctcctg caggaagggg cgtcgccggt ggtggcgctg 480 aagcggcggc actccatgcg agcggcagca gcggggcggc ggcgcaagag cgctgcacct 540 gcaccggcgg atcaggaagg cggaggaggg gtgatggagc tggaggacct gggacctgac 600 tacctggagg agctgctagc cgcctctcag cccatcgata tcacctgctg cacaagccca 660 agccaccact ccatctga 678 18 225 PRT Oryza sativa 18 Met His Cys Cys Met Ser Leu His Pro His Arg Arg His Gly Asp Gly 1 5 10 15 Asp Val Asp Gly Ser Ala Ser Gly Ser Gly Ser Ala Arg Leu Thr Ala 20 25 30 Gly Leu Ile Asn Phe Leu Glu Ser Arg Arg Ala Gly Ala Met Ser Thr 35 40 45 Thr Asn Ser Ser Ser Ser Val Ser Val Pro Ala Met Asp Ala His Gly 50 55 60 Gln Glu Glu Glu Glu Glu Pro Met Gln Val Gln Gln Gln Gln Ala Phe 65 70 75 80 Arg Gly Val Arg Lys Arg Pro Trp Gly Lys Phe Ala Ala Glu Ile Arg 85 90 95 Asp Ser Thr Arg Asn Gly Val Arg Val Trp Leu Gly Thr Phe Asp Ser 100 105 110 Ala Glu Glu Ala Ala Leu Ala Tyr Asp Gln Ala Ala Phe Ala Met Arg 115 120 125 Gly Ser Ala Ala Val Leu Asn Phe Pro Met Glu Gln Val Arg Arg Ser 130 135 140 Met Asp Met Ser Leu Leu Gln Glu Gly Ala Ser Pro Val Val Ala Leu 145 150 155 160 Lys Arg Arg His Ser Met Arg Ala Ala Ala Ala Gly Arg Arg Arg Lys 165 170 175 Ser Ala Ala Pro Ala Pro Ala Asp Gln Glu Gly Gly Gly Gly Val Met 180 185 190 Glu Leu Glu Asp Leu Gly Pro Asp Tyr Leu Glu Glu Leu Leu Ala Ala 195 200 205 Ser Gln Pro Ile Asp Ile Thr Cys Cys Thr Ser Pro Ser His His Ser 210 215 220 Ile 225 19 588 DNA Oryza sativa 19 atgatctacc cgccactgta ccgctgcaac gacgaggtga agcagtgcgc cgccgcctgc 60 aaggagtgcg tggaggcgcc cggcggcgac ttcaacggcg gcgccttcgt ctgcagtgac 120 tggttctcga cggtggaccc cggccccaag tgcacggcgg cgctggatgg gctgtcgatg 180 gagaggccgt ggaagtgctg cgacaacatc aagcggctgc cgacgaagcc cgacccgccg 240 cagtggcgct gcaacgacga gctggagccc agccagtgca ccgccgcgtg caagtcgtgc 300 cgggaggcgc cggggccatt cccggggaag ctcatctgcg aggacatcta ctggggcgcc 360 gacccgggcc ccttctgcac gccgcggcca tggggagatt gctacgacaa ggccttctgc 420 aacaagatga acccgccgac ctgccgctgc atggacgagg tgaaggagtg cgccgacgcg 480 tgcaaggatt gccagcgcgt ggagtcgtcg gagccgcctc gctacgtctg caaggaccgc 540 ttcaccggcc atcccggccc cgtgtgcaaa ccccgagcgg agaactag 588 20 195 PRT Oryza sativa 20 Met Ile Tyr Pro Pro Leu Tyr Arg Cys Asn Asp Glu Val Lys Gln Cys 1 5 10 15 Ala Ala Ala Cys Lys Glu Cys Val Glu Ala Pro Gly Gly Asp Phe Asn 20 25 30 Gly Gly Ala Phe Val Cys Ser Asp Trp Phe Ser Thr Val Asp Pro Gly 35 40 45 Pro Lys Cys Thr Ala Ala Leu Asp Gly Leu Ser Met Glu Arg Pro Trp 50 55 60 Lys Cys Cys Asp Asn Ile Lys Arg Leu Pro Thr Lys Pro Asp Pro Pro 65 70 75 80 Gln Trp Arg Cys Asn Asp Glu Leu Glu Pro Ser Gln Cys Thr Ala Ala 85 90 95 Cys Lys Ser Cys Arg Glu Ala Pro Gly Pro Phe Pro Gly Lys Leu Ile 100 105 110 Cys Glu Asp Ile Tyr Trp Gly Ala Asp Pro Gly Pro Phe Cys Thr Pro 115 120 125 Arg Pro Trp Gly Asp Cys Tyr Asp Lys Ala Phe Cys Asn Lys Met Asn 130 135 140 Pro Pro Thr Cys Arg Cys Met Asp Glu Val Lys Glu Cys Ala Asp Ala 145 150 155 160 Cys Lys Asp Cys Gln Arg Val Glu Ser Ser Glu Pro Pro Arg Tyr Val 165 170 175 Cys Lys Asp Arg Phe Thr Gly His Pro Gly Pro Val Cys Lys Pro Arg 180 185 190 Ala Glu Asn 195 21 2775 DNA Oryza sativa 21 atgttgcgtc ctcagctcaa tccatctagc cacacgacga cgacgagcag cagcagcagc 60 acgcagctgt tcgcatcctc gtcgtgcatc gctagccttc gccggccgtc gtcgtcgtcg 120 tcgtcggtgg tcgccgccgc acgccggacg cgggggcaag gtagcagtcg ggttgttgtt 180 gtgtgcgcgt cgtcgtcggc gacggcgagc aggggagata gttcttcgga catggcggcg 240 gcggcggcgg tgcgggtgaa ggcggtggcg acgatcaagg tcaccgtcgg cgagttgatc 300 aacaggtcga tcgacatcag ggatctcatc ggcaggtcgc tctccctcga gctcgtcagc 360 tccgagcttg acgcgaagac cgggaaggag aaagcaactg tgcggagcta cgcgcacaat 420 gtggacgacg acgatcatag cgtcgtcacc tacgaggccg acttcgacgt gccgagtgga 480 ttcggcccca tcggcgccat catcgtcacc aacgaactcc ggcaggagat gttcctcgag 540 gacatcaacc tcaccgccag cgatggcgcc ggcaactcca ctgtcctccc catccgctgc 600 aactcctggg tccaacccaa gtccgtcggc gatgagggca cgcctagcaa acgcatcttc 660 ttcgccaaca agacttactt gccgggacag acgccggcgg ggctccggag ctaccggaag 720 aatgacctcc agcagaagcg cggtgacggc actggcgaga gggaggccga cgaccgtgtc 780 tacgactacg acgtttacaa cgacctcggt aacccggaca gcaacggcga tctcgcccgc 840 cccgtccttg gcggcaacaa gcagttcccc taccctcgcc gctgccgcac cggccgcccc 900 ccctccaaaa aagaccctaa gtcggagacg aggaagggca acgtgtacgt gccgagggac 960 gaggagttct caccggagaa ggaggactac ttcctccgca agacggtggg gtcggtgctc 1020 caggccgccg tgccggcggc gcagtcgctg ctcctcgaca agctgaaatg gaaccttccg 1080 ttcccgtcct tcttcgtcat cgacaagctg ttcgaggacg gcgtcgagct tcccggcgtc 1140 gacaagctca acttcctcga gagcgtcgtg ccccgcctgc tcgaacacct ccgcgacacc 1200 cccgccgaga agatcctccg cttcgaaact ccggccaaca tccaaaagga caagttcgca 1260 tggctcagag acgaggagtt cgcgagggaa acgctcgctg gcatcaaccc gtacgccatc 1320 gagctcgtca gggaatttcc gctgaagagc aagctcgacc cggcggtgta cggtccggcg 1380 gagtcggcga tcaccgccga tttgctggag gagcagatga ggcgcgtgat gacggtggag 1440 gaggcgatca gccagaagag gctgttcatg ctcgacttcc atgacctctt cttgccgtac 1500 gtgcacaaga tccggtcgct ggatcacacc accatgtacg gctcgcgcac cgtcttcttc 1560 ctcaccgacg acggcacgct gcagctgctc gccatcgagc tcacccggcc ggcctcgccg 1620 tcgcagccgc agtggcggca ggtgttcacg ccgtccacgg acgccaccat gtcgtggctg 1680 tggcggatgg ccaaggccca cgtccgcgcc cacgacgccg gccaccacga gctcatcacc 1740 cactggctgc gcacgcactg cgcggtggag ccatacatca tcgcggcgaa ccggcagctc 1800 agcgagatgc accccatcta ccagctgctg cgcccgcact tccgctacac gatgcggatc 1860 aacgcgcgcg cccgctcggc gctgatcagc gccggcggca tcatcgagcg atccttctcg 1920 ccgcagaagt actccatgga gctcagctcc gtcgcctacg acaagctctg gcgcttcgac 1980 acggaggcgc tccccgccga cctcgtccgc cgcggcatgg ccgaggagga ccccacggcg 2040 gagcacggcc tcaagctcgc catcgaggac tacccgttcg ccaacgacgg cctcctcatc 2100 tgggacgcca tcaagacctg ggtccaggcg tacgtcgcgc ggttctaccc cgacgccgac 2160 agcgtcgccg gcgacgagga gctccaggcg ttctggaccg aggtgcgcac caaggggcac 2220 ggcgacaaga aggacgcccc gtggtggccg aagttggact cgccggagag cctcgcccac 2280 acgctgacca ccatcgtctg ggtggcggcg gcgcaccacg ccgccgtcaa cttcgggcag 2340 tacgacttcg gcggctactt ccccaaccgg ccgtccatcg cgcgcacggt catgccggtg 2400 gaggagcccg tggacggcgc cgccatggag aggttcctgg acaacccgga ccaggcgctc 2460 cgcgagtgct tcccgtcaca ggtgcaggcg acggtggtga tggcggtgct cgacgtgctg 2520 tccagccact ccaccgacga ggagtacctc ggcggcgagc agacgaggcc gtggaacagc 2580 gacgcggcgg tgcaggcggc gtacgacggg ttcgcagccc ggctcaagga gatcgagggc 2640 gtcatcgatg gccggaacaa ggatagaaag ctcaagaaca ggtgcggcgc cggcatcctg 2700 ccgtaccagc tgatgaagcc cttctccgac tccggcgtca ccggcatggg catccccaac 2760 agcacatcca tctga 2775 22 924 PRT Oryza sativa 22 Met Leu Arg Pro Gln Leu Asn Pro Ser Ser His Thr Thr Thr Thr Ser 1 5 10 15 Ser Ser Ser Ser Thr Gln Leu Phe Ala Ser Ser Ser Cys Ile Ala Ser 20 25 30 Leu Arg Arg Pro Ser Ser Ser Ser Ser Ser Val Val Ala Ala Ala Arg 35 40 45 Arg Thr Arg Gly Gln Gly Ser Ser Arg Val Val Val Val Cys Ala Ser 50 55 60 Ser Ser Ala Thr Ala Ser Arg Gly Asp Ser Ser Ser Asp Met Ala Ala 65 70 75 80 Ala Ala Ala Val Arg Val Lys Ala Val Ala Thr Ile Lys Val Thr Val 85 90 95 Gly Glu Leu Ile Asn Arg Ser Ile Asp Ile Arg Asp Leu Ile Gly Arg 100 105 110 Ser Leu Ser Leu Glu Leu Val Ser Ser Glu Leu Asp Ala Lys Thr Gly 115 120 125 Lys Glu Lys Ala Thr Val Arg Ser Tyr Ala His Asn Val Asp Asp Asp 130 135 140 Asp His Ser Val Val Thr Tyr Glu Ala Asp Phe Asp Val Pro Ser Gly 145 150 155 160 Phe Gly Pro Ile Gly Ala Ile Ile Val Thr Asn Glu Leu Arg Gln Glu 165 170 175 Met Phe Leu Glu Asp Ile Asn Leu Thr Ala Ser Asp Gly Ala Gly Asn 180 185 190 Ser Thr Val Leu Pro Ile Arg Cys Asn Ser Trp Val Gln Pro Lys Ser 195 200 205 Val Gly Asp Glu Gly Thr Pro Ser Lys Arg Ile Phe Phe Ala Asn Lys 210 215 220 Thr Tyr Leu Pro Gly Gln Thr Pro Ala Gly Leu Arg Ser Tyr Arg Lys 225 230 235 240 Asn Asp Leu Gln Gln Lys Arg Gly Asp Gly Thr Gly Glu Arg Glu Ala 245 250 255 Asp Asp Arg Val Tyr Asp Tyr Asp Val Tyr Asn Asp Leu Gly Asn Pro 260 265 270 Asp Ser Asn Gly Asp Leu Ala Arg Pro Val Leu Gly Gly Asn Lys Gln 275 280 285 Phe Pro Tyr Pro Arg Arg Cys Arg Thr Gly Arg Pro Pro Ser Lys Lys 290 295 300 Asp Pro Lys Ser Glu Thr Arg Lys Gly Asn Val Tyr Val Pro Arg Asp 305 310 315 320 Glu Glu Phe Ser Pro Glu Lys Glu Asp Tyr Phe Leu Arg Lys Thr Val 325 330 335 Gly Ser Val Leu Gln Ala Ala Val Pro Ala Ala Gln Ser Leu Leu Leu 340 345 350 Asp Lys Leu Lys Trp Asn Leu Pro Phe Pro Ser Phe Phe Val Ile Asp 355 360 365 Lys Leu Phe Glu Asp Gly Val Glu Leu Pro Gly Val Asp Lys Leu Asn 370 375 380 Phe Leu Glu Ser Val Val Pro Arg Leu Leu Glu His Leu Arg Asp Thr 385 390 395 400 Pro Ala Glu Lys Ile Leu Arg Phe Glu Thr Pro Ala Asn Ile Gln Lys 405 410 415 Asp Lys Phe Ala Trp Leu Arg Asp Glu Glu Phe Ala Arg Glu Thr Leu 420 425 430 Ala Gly Ile Asn Pro Tyr Ala Ile Glu Leu Val Arg Glu Phe Pro Leu 435 440 445 Lys Ser Lys Leu Asp Pro Ala Val Tyr Gly Pro Ala Glu Ser Ala Ile 450 455 460 Thr Ala Asp Leu Leu Glu Glu Gln Met Arg Arg Val Met Thr Val Glu 465 470 475 480 Glu Ala Ile Ser Gln Lys Arg Leu Phe Met Leu Asp Phe His Asp Leu 485 490 495 Phe Leu Pro Tyr Val His Lys Ile Arg Ser Leu Asp His Thr Thr Met 500 505 510 Tyr Gly Ser Arg Thr Val Phe Phe Leu Thr Asp Asp Gly Thr Leu Gln 515 520 525 Leu Leu Ala Ile Glu Leu Thr Arg Pro Ala Ser Pro Ser Gln Pro Gln 530 535 540 Trp Arg Gln Val Phe Thr Pro Ser Thr Asp Ala Thr Met Ser Trp Leu 545 550 555 560 Trp Arg Met Ala Lys Ala His Val Arg Ala His Asp Ala Gly His His 565 570 575 Glu Leu Ile Thr His Trp Leu Arg Thr His Cys Ala Val Glu Pro Tyr 580 585 590 Ile Ile Ala Ala Asn Arg Gln Leu Ser Glu Met His Pro Ile Tyr Gln 595 600 605 Leu Leu Arg Pro His Phe Arg Tyr Thr Met Arg Ile Asn Ala Arg Ala 610 615 620 Arg Ser Ala Leu Ile Ser Ala Gly Gly Ile Ile Glu Arg Ser Phe Ser 625 630 635 640 Pro Gln Lys Tyr Ser Met Glu Leu Ser Ser Val Ala Tyr Asp Lys Leu 645 650 655 Trp Arg Phe Asp Thr Glu Ala Leu Pro Ala Asp Leu Val Arg Arg Gly 660 665 670 Met Ala Glu Glu Asp Pro Thr Ala Glu His Gly Leu Lys Leu Ala Ile 675 680 685 Glu Asp Tyr Pro Phe Ala Asn Asp Gly Leu Leu Ile Trp Asp Ala Ile 690 695 700 Lys Thr Trp Val Gln Ala Tyr Val Ala Arg Phe Tyr Pro Asp Ala Asp 705 710 715 720 Ser Val Ala Gly Asp Glu Glu Leu Gln Ala Phe Trp Thr Glu Val Arg 725 730 735 Thr Lys Gly His Gly Asp Lys Lys Asp Ala Pro Trp Trp Pro Lys Leu 740 745 750 Asp Ser Pro Glu Ser Leu Ala His Thr Leu Thr Thr Ile Val Trp Val 755 760 765 Ala Ala Ala His His Ala Ala Val Asn Phe Gly Gln Tyr Asp Phe Gly 770 775 780 Gly Tyr Phe Pro Asn Arg Pro Ser Ile Ala Arg Thr Val Met Pro Val 785 790 795 800 Glu Glu Pro Val Asp Gly Ala Ala Met Glu Arg Phe Leu Asp Asn Pro 805 810 815 Asp Gln Ala Leu Arg Glu Cys Phe Pro Ser Gln Val Gln Ala Thr Val 820 825 830 Val Met Ala Val Leu Asp Val Leu Ser Ser His Ser Thr Asp Glu Glu 835 840 845 Tyr Leu Gly Gly Glu Gln Thr Arg Pro Trp Asn Ser Asp Ala Ala Val 850 855 860 Gln Ala Ala Tyr Asp Gly Phe Ala Ala Arg Leu Lys Glu Ile Glu Gly 865 870 875 880 Val Ile Asp Gly Arg Asn Lys Asp Arg Lys Leu Lys Asn Arg Cys Gly 885 890 895 Ala Gly Ile Leu Pro Tyr Gln Leu Met Lys Pro Phe Ser Asp Ser Gly 900 905 910 Val Thr Gly Met Gly Ile Pro Asn Ser Thr Ser Ile 915 920 23 1797 DNA Oryza sativa 23 atgggcacgt acaagtgctg cctcatcttc aagcgccgct tccgctggaa cgacgcgccg 60 ccgcccgacg atgtccgcgc cctcttcgcc aaccactccg ccggcggtgg cccccacatg 120 gccgccgacg gcctccgcgc ctacctccag gccaccggcc aggacggcga cgtggacatg 180 gagcggctgg tggagcagat ccggcagctg caggggcgcg gcgggcgcat cccgcgggtg 240 gggcgggcac tcccactcct gacggtggac gacttccacc gattcctctt ctcccacgag 300 ctgaacccac ccatccggca cgggcagggg caggtgcacc acgacatggc cgccccgctc 360 tcccactact tcatctacac cggccacaac tcctacctca ccggcaacca gctcagcagc 420 gactgcagcg acctccccat catcagggct ctccagaggg gcgtccgcgt catcgagctc 480 gacatgtggc ccaactcctc caaggatgac atcagcatcc tccatggcag gacgctcacc 540 accccggtct ccctcctcaa atgcctcctc tccatcaagc aacacgcctt tgaggcctcc 600 ccttacccgg ttatcatcac gctcgaagac cacctcaccc ccgatctcca ggacaaagca 660 gccaagatgg ttcttgaagt tttcggcgac atcctctact accctgacaa agatcacctc 720 aaagagttcc cttcgcctca agacctcaag ggccgtgtcc tcctctccac caagcccccc 780 agggagtacc ttcaagccaa ggatggtaat gctgccacca tcaaagagga cgccaaggcc 840 gccgccactg acgatgccgc atggggaaaa gaagtcccag atattcactc tcaaatccac 900 tctgccacta aacatgacca aagagaagat gacgacgaca ccgatgaaga cgaagatgac 960 gaggaggagg agcagaaaat gcaacagcat ctagctccac agtacaaaca ccttattacc 1020 atcaaagcag gaaagccaaa aggtactcta cttgatgcct tacagagtga cccagaaaag 1080 gttagaaggc tcagtttgag cgagcaacaa cttgccaaat tggcagatca tcatggtacc 1140 gaaattgtaa ggttcacaca gagaaaccta ctgaggatat acccaaaggg cactcgggtc 1200 acatcatcca actataatcc atttcttggt tgggtgcatg gtgctcagat ggtagcgttc 1260 aatatgcagg gatatggaag agctctttgg ttgatgcatg gattttataa agctaatggt 1320 ggctgtggtt atgtgaagaa accagatttc ttaatgcaaa ctgatccaga ggtttttgac 1380 ccaaaaaaat ccctatctcc caagaaaacc ttgaaggtga aagtatacat gggggatggt 1440 tggcggatgg acttcacgca gacccacttt gatcaatatt ctcctccaga cttttatgca 1500 cgggtgggga tagcgggagt accagcggac tcggtgatga agagaacgag ggcgatagag 1560 gataactggg tgccggtgtg ggaggaggat ttcaccttca aactgaccgt gccggagatc 1620 gcgttgctgc gggtggaggt gcacgagtac gacatgtcgg agaaggacga cttcggcggc 1680 cagacggtgc tgccggtgtc ggatctcatc ccggggatcc gagcggtggc actccacgac 1740 cgcaaaggga tcaagttgaa caacgtcaag cttctcatgc gcttcgagtt tgaatga 1797 24 598 PRT Oryza sativa 24 Met Gly Thr Tyr Lys Cys Cys Leu Ile Phe Lys Arg Arg Phe Arg Trp 1 5 10 15 Asn Asp Ala Pro Pro Pro Asp Asp Val Arg Ala Leu Phe Ala Asn His 20 25 30 Ser Ala Gly Gly Gly Pro His Met Ala Ala Asp Gly Leu Arg Ala Tyr 35 40 45 Leu Gln Ala Thr Gly Gln Asp Gly Asp Val Asp Met Glu Arg Leu Val 50 55 60 Glu Gln Ile Arg Gln Leu Gln Gly Arg Gly Gly Arg Ile Pro Arg Val 65 70 75 80 Gly Arg Ala Leu Pro Leu Leu Thr Val Asp Asp Phe His Arg Phe Leu 85 90 95 Phe Ser His Glu Leu Asn Pro Pro Ile Arg His Gly Gln Gly Gln Val 100 105 110 His His Asp Met Ala Ala Pro Leu Ser His Tyr Phe Ile Tyr Thr Gly 115 120 125 His Asn Ser Tyr Leu Thr Gly Asn Gln Leu Ser Ser Asp Cys Ser Asp 130 135 140 Leu Pro Ile Ile Arg Ala Leu Gln Arg Gly Val Arg Val Ile Glu Leu 145 150 155 160 Asp Met Trp Pro Asn Ser Ser Lys Asp Asp Ile Ser Ile Leu His Gly 165 170 175 Arg Thr Leu Thr Thr Pro Val Ser Leu Leu Lys Cys Leu Leu Ser Ile 180 185 190 Lys Gln His Ala Phe Glu Ala Ser Pro Tyr Pro Val Ile Ile Thr Leu 195 200 205 Glu Asp His Leu Thr Pro Asp Leu Gln Asp Lys Ala Ala Lys Met Val 210 215 220 Leu Glu Val Phe Gly Asp Ile Leu Tyr Tyr Pro Asp Lys Asp His Leu 225 230 235 240 Lys Glu Phe Pro Ser Pro Gln Asp Leu Lys Gly Arg Val Leu Leu Ser 245 250 255 Thr Lys Pro Pro Arg Glu Tyr Leu Gln Ala Lys Asp Gly Asn Ala Ala 260 265 270 Thr Ile Lys Glu Asp Ala Lys Ala Ala Ala Thr Asp Asp Ala Ala Trp 275 280 285 Gly Lys Glu Val Pro Asp Ile His Ser Gln Ile His Ser Ala Thr Lys 290 295 300 His Asp Gln Arg Glu Asp Asp Asp Asp Thr Asp Glu Asp Glu Asp Asp 305 310 315 320 Glu Glu Glu Glu Gln Lys Met Gln Gln His Leu Ala Pro Gln Tyr Lys 325 330 335 His Leu Ile Thr Ile Lys Ala Gly Lys Pro Lys Gly Thr Leu Leu Asp 340 345 350 Ala Leu Gln Ser Asp Pro Glu Lys Val Arg Arg Leu Ser Leu Ser Glu 355 360 365 Gln Gln Leu Ala Lys Leu Ala Asp His His Gly Thr Glu Ile Val Arg 370 375 380 Phe Thr Gln Arg Asn Leu Leu Arg Ile Tyr Pro Lys Gly Thr Arg Val 385 390 395 400 Thr Ser Ser Asn Tyr Asn Pro Phe Leu Gly Trp Val His Gly Ala Gln 405 410 415 Met Val Ala Phe Asn Met Gln Gly Tyr Gly Arg Ala Leu Trp Leu Met 420 425 430 His Gly Phe Tyr Lys Ala Asn Gly Gly Cys Gly Tyr Val Lys Lys Pro 435 440 445 Asp Phe Leu Met Gln Thr Asp Pro Glu Val Phe Asp Pro Lys Lys Ser 450 455 460 Leu Ser Pro Lys Lys Thr Leu Lys Val Lys Val Tyr Met Gly Asp Gly 465 470 475 480 Trp Arg Met Asp Phe Thr Gln Thr His Phe Asp Gln Tyr Ser Pro Pro 485 490 495 Asp Phe Tyr Ala Arg Val Gly Ile Ala Gly Val Pro Ala Asp Ser Val 500 505 510 Met Lys Arg Thr Arg Ala Ile Glu Asp Asn Trp Val Pro Val Trp Glu 515 520 525 Glu Asp Phe Thr Phe Lys Leu Thr Val Pro Glu Ile Ala Leu Leu Arg 530 535 540 Val Glu Val His Glu Tyr Asp Met Ser Glu Lys Asp Asp Phe Gly Gly 545 550 555 560 Gln Thr Val Leu Pro Val Ser Asp Leu Ile Pro Gly Ile Arg Ala Val 565 570 575 Ala Leu His Asp Arg Lys Gly Ile Lys Leu Asn Asn Val Lys Leu Leu 580 585 590 Met Arg Phe Glu Phe Glu 595 25 1140 DNA Oryza sativa 25 atggcagcga cgatggtggc gatgtcggcc aagagcaaga acagcgtgct gacattggag 60 aagaagcagg gctggtctgt cccacaactt ccggagctcc ggttcccttg ggatttgcat 120 gaagacaagg gcttctcttt gagcttacat ggctctgcct cccctcatgg tgggctgttt 180 gctagcgtcg gtctcaaagt gtccacagct gcaccagcag tggcacccag tcctgccgag 240 catgacttca agattccgtt cgctgatcat tgcataaagt atgtctcctc agcagtgggg 300 taccaagttc ctgggactga ggctgaatct gtcaatgagg aagaggtggt ggatggcaag 360 gctgtgaaga aagccaagaa acgtgggctg aagctgaaaa ttaagattgg gaacccacat 420 ttgaggcggc tggttagcgg agccgttgcg ggagctgtct cgaggacttg tgtggcacct 480 ctggagacga ttaggaccca tttgatggtt gggagcaatg gggactctat gacagaggta 540 ttccagtcaa tcatgaagac cgaggggtgg acagggctgt tccgtgggaa ctttgtcaat 600 gtcatccgag ttgcaccaag caaggctatt gagctatttg ctttcgatac agccaagaaa 660 ttcttaactc caaaggctga tgagtcccct aagacaccct tccctccatc gcttattgct 720 ggagcacttg ctggggttag ctcaacattg tgcacatacc ccttggaatt gatcaagacc 780 cgattgacta ttgagaaaga tgtctataac aacttcctcc atgctttcgt caagatacta 840 cgagaggaag gcccctcagc tctaccgcgg gctgacaccg agtctgatcg gcgtggtgcc 900 atacgctgca accaattact atgcctacga caccctgaag aagctctaca ggaagacatt 960 caagcaggag gagatcagca acatcgcgac tcttctcatc ggttcagccg cgggtgccat 1020 ctcgagcacc gccaccttcc ctctcgaggt agctcgcaag caaatgcagg tcggagcggt 1080 aggcggcagg caggtctaca agaatgtctt ccatgctctg tattgcataa tggagaatga 1140 26 379 PRT Oryza sativa 26 Met Ala Ala Thr Met Val Ala Met Ser Ala Lys Ser Lys Asn Ser Val 1 5 10 15 Leu Thr Leu Glu Lys Lys Gln Gly Trp Ser Val Pro Gln Leu Pro Glu 20 25 30 Leu Arg Phe Pro Trp Asp Leu His Glu Asp Lys Gly Phe Ser Leu Ser 35 40 45 Leu His Gly Ser Ala Ser Pro His Gly Gly Leu Phe Ala Ser Val Gly 50 55 60 Leu Lys Val Ser Thr Ala Ala Pro Ala Val Ala Pro Ser Pro Ala Glu 65 70 75 80 His Asp Phe Lys Ile Pro Phe Ala Asp His Cys Ile Lys Tyr Val Ser 85 90 95 Ser Ala Val Gly Tyr Gln Val Pro Gly Thr Glu Ala Glu Ser Val Asn 100 105 110 Glu Glu Glu Val Val Asp Gly Lys Ala Val Lys Lys Ala Lys Lys Arg 115 120 125 Gly Leu Lys Leu Lys Ile Lys Ile Gly Asn Pro His Leu Arg Arg Leu 130 135 140 Val Ser Gly Ala Val Ala Gly Ala Val Ser Arg Thr Cys Val Ala Pro 145 150 155 160 Leu Glu Thr Ile Arg Thr His Leu Met Val Gly Ser Asn Gly Asp Ser 165 170 175 Met Thr Glu Val Phe Gln Ser Ile Met Lys Thr Glu Gly Trp Thr Gly 180 185 190 Leu Phe Arg Gly Asn Phe Val Asn Val Ile Arg Val Ala Pro Ser Lys 195 200 205 Ala Ile Glu Leu Phe Ala Phe Asp Thr Ala Lys Lys Phe Leu Thr Pro 210 215 220 Lys Ala Asp Glu Ser Pro Lys Thr Pro Phe Pro Pro Ser Leu Ile Ala 225 230 235 240 Gly Ala Leu Ala Gly Val Ser Ser Thr Leu Cys Thr Tyr Pro Leu Glu 245 250 255 Leu Ile Lys Thr Arg Leu Thr Ile Glu Lys Asp Val Tyr Asn Asn Phe 260 265 270 Leu His Ala Phe Val Lys Ile Leu Arg Glu Glu Gly Pro Ser Ala Leu 275 280 285 Pro Arg Ala Asp Thr Glu Ser Asp Arg Arg Gly Ala Ile Arg Cys Asn 290 295 300 Gln Leu Leu Cys Leu Arg His Pro Glu Glu Ala Leu Gln Glu Asp Ile 305 310 315 320 Gln Ala Gly Gly Asp Gln Gln His Arg Asp Ser Ser His Arg Phe Ser 325 330 335 Arg Gly Cys His Leu Glu His Arg His Leu Pro Ser Arg Gly Ser Ser 340 345 350 Gln Ala Asn Ala Gly Arg Ser Gly Arg Arg Gln Ala Gly Leu Gln Glu 355 360 365 Cys Leu Pro Cys Ser Val Leu His Asn Gly Glu 370 375 27 1488 DNA Oryza sativa 27 atgccgtggc cgcacgtgct gacggtggcc ggctccgact ccggcggcgg cgccggcatc 60 caggccgaca tcaaggcctg cgccgcgctg ggagcctact gctcctccgt cgtcaccgcc 120 gtcactgccc agaacaccgc cggcgtccag gggactcatg tggtgccaga ggagttcatc 180 cgggagcagc tcaactcggt tctttcggac atgtcggtgg atgtggtcaa gacaggaatg 240 ctcccttcaa tcggagtagt cggagtttta tgtgaaagtc taaagaagtt tccagtcaaa 300 gctttagtgg tggatccagt tatggtgtcc acaagtggag atactctttc agaatcatct 360 actctctctg tatataggga tgaattattt gctatggctg atatagtcac cccaaatgtg 420 aaagaagcgt cgagattact tgggggtgta tctttgcgca ctgtttctga catgcgcaat 480 gcagcggagt ccatttacaa atttggtcca aaacatgtac ttgtgaaagg tggggatatg 540 ctagaatcct cagatgcaac tgatgtattt tttgatggta aggagttcat tgagctccat 600 gcgcatcgca taaagaccca taacacacat ggaactggtt gcactttagc ttcatgtata 660 gcttccgaat tagcgaaagg tgcaacgatg ctgcatgctg ttcaggtggc taagaatttt 720 gtagaatctg ctcttcatca cagtaaagat cttgtcgttg gaaatggacc tcaaggccct 780 tttgatcacc ttttcaagct caagtgtccg ccatacaatg ttggctcaca gccaagcttt 840 aagccagacc aactcttcct gtatgcagtg acagactctg ggatgaacaa aaagtggggt 900 cgttcaatca aagaagctgt gcaagctgcc attgaaggtg gcgctaccat tgtacaactg 960 agagaaaaag attccgaaac aagagagttt ttggaagcag ccaaagcatg catggagatt 1020 tgcaagtcca gtggagtacc actgctgatc aacgaccggg tagacattgc cctggcacgc 1080 aatgcagatg gtgtccatgt tggtcaattg gacatgtcgg cacacgaagt gcgggagctc 1140 ctagggccgg gtaaaatcat cggcgtctcg tgcaagaccc ctgctcaagc ccagcaggcc 1200 tggaatgatg gagcagacta cattggctgt ggcggtgttt tccctacctc cacgaaggcg 1260 aacaatccta cattggggtt tgatggcttg aagacagttt gcctggcatc taagctgcct 1320 gtggtcgcta ttggcggcat caacgcttca aatgcaggtt cagtgatgga gcttggtctc 1380 ccaaacctca aaggcgtcgc agtagtctcc gctctgtttg accgtccgag tgtcgtagcc 1440 gaaacaagaa acatgaaatc catcttgacc aacacctcta gaacctag 1488 28 495 PRT Oryza sativa 28 Met Pro Trp Pro His Val Leu Thr Val Ala Gly Ser Asp Ser Gly Gly 1 5 10 15 Gly Ala Gly Ile Gln Ala Asp Ile Lys Ala Cys Ala Ala Leu Gly Ala 20 25 30 Tyr Cys Ser Ser Val Val Thr Ala Val Thr Ala Gln Asn Thr Ala Gly 35 40 45 Val Gln Gly Thr His Val Val Pro Glu Glu Phe Ile Arg Glu Gln Leu 50 55 60 Asn Ser Val Leu Ser Asp Met Ser Val Asp Val Val Lys Thr Gly Met 65 70 75 80 Leu Pro Ser Ile Gly Val Val Gly Val Leu Cys Glu Ser Leu Lys Lys 85 90 95 Phe Pro Val Lys Ala Leu Val Val Asp Pro Val Met Val Ser Thr Ser 100 105 110 Gly Asp Thr Leu Ser Glu Ser Ser Thr Leu Ser Val Tyr Arg Asp Glu 115 120 125 Leu Phe Ala Met Ala Asp Ile Val Thr Pro Asn Val Lys Glu Ala Ser 130 135 140 Arg Leu Leu Gly Gly Val Ser Leu Arg Thr Val Ser Asp Met Arg Asn 145 150 155 160 Ala Ala Glu Ser Ile Tyr Lys Phe Gly Pro Lys His Val Leu Val Lys 165 170 175 Gly Gly Asp Met Leu Glu Ser Ser Asp Ala Thr Asp Val Phe Phe Asp 180 185 190 Gly Lys Glu Phe Ile Glu Leu His Ala His Arg Ile Lys Thr His Asn 195 200 205 Thr His Gly Thr Gly Cys Thr Leu Ala Ser Cys Ile Ala Ser Glu Leu 210 215 220 Ala Lys Gly Ala Thr Met Leu His Ala Val Gln Val Ala Lys Asn Phe 225 230 235 240 Val Glu Ser Ala Leu His His Ser Lys Asp Leu Val Val Gly Asn Gly 245 250 255 Pro Gln Gly Pro Phe Asp His Leu Phe Lys Leu Lys Cys Pro Pro Tyr 260 265 270 Asn Val Gly Ser Gln Pro Ser Phe Lys Pro Asp Gln Leu Phe Leu Tyr 275 280 285 Ala Val Thr Asp Ser Gly Met Asn Lys Lys Trp Gly Arg Ser Ile Lys 290 295 300 Glu Ala Val Gln Ala Ala Ile Glu Gly Gly Ala Thr Ile Val Gln Leu 305 310 315 320 Arg Glu Lys Asp Ser Glu Thr Arg Glu Phe Leu Glu Ala Ala Lys Ala 325 330 335 Cys Met Glu Ile Cys Lys Ser Ser Gly Val Pro Leu Leu Ile Asn Asp 340 345 350 Arg Val Asp Ile Ala Leu Ala Arg Asn Ala Asp Gly Val His Val Gly 355 360 365 Gln Leu Asp Met Ser Ala His Glu Val Arg Glu Leu Leu Gly Pro Gly 370 375 380 Lys Ile Ile Gly Val Ser Cys Lys Thr Pro Ala Gln Ala Gln Gln Ala 385 390 395 400 Trp Asn Asp Gly Ala Asp Tyr Ile Gly Cys Gly Gly Val Phe Pro Thr 405 410 415 Ser Thr Lys Ala Asn Asn Pro Thr Leu Gly Phe Asp Gly Leu Lys Thr 420 425 430 Val Cys Leu Ala Ser Lys Leu Pro Val Val Ala Ile Gly Gly Ile Asn 435 440 445 Ala Ser Asn Ala Gly Ser Val Met Glu Leu Gly Leu Pro Asn Leu Lys 450 455 460 Gly Val Ala Val Val Ser Ala Leu Phe Asp Arg Pro Ser Val Val Ala 465 470 475 480 Glu Thr Arg Asn Met Lys Ser Ile Leu Thr Asn Thr Ser Arg Thr 485 490 495 29 1143 DNA Oryza sativa 29 atggcgtcgc tgctgatcgc cagcacgggg ggcgcccacc gcctcgcgtg gaaggacgcc 60 gccgccctgg gacccgctcc gcggctggcg cgaccttggc ccgccgccgt ggctgcaccg 120 gcgccgctgc tcaggattag cagaggaaag tttgcattgc aggccatcac ccttgatgat 180 tatcttccaa tgcgaagtac tgaagtgaaa aatcggacat caacagctga tatcactagt 240 ctcagagtaa ttacagcggt caaaacccca tatctgcctg atggaagatt tgatcttgaa 300 gcatatgatt cactgataaa tatgcagata gatggtggtg ctgaaggtgt aatagttgga 360 ggaacaacag gagagggcca ccttatgagc tgggatgaac acatcatgct tattggacat 420 actgttaact gctttggtgc taaagttaaa gtggtaggca acacaggtag taactcaaca 480 agagaggcta ttcatgcaac agagcaggga tttgctgtag gtatgcatgc ggctctccat 540 atcaatcctt actatgggaa gacctctatc gaagggttga tatctcattt tgaggctgtc 600 ctcccaatgg gtccaaccat tatttacaat gttccatcta ggactggcca ggatattcct 660 cctgcagtta ttgaggctgt ttcaagtttc acaaacttgg caggtgtgaa agaatgtgtt 720 ggacatgaga gggttaagtg ctacactgac aaaggtataa ccatatggag tggtaatgat 780 gatgaatgcc atgattctag gtggaaatat ggtgccactg gagttatttc tgtggctagc 840 aaccttattc ctggtctcat gcacgatctc atgtatgaag gggagaataa gacgctaaat 900 gagaagctct ttcccctgat gaaatggttg ttttgccagc caaatccaat tgctctcaac 960 actgccctgg ctcagcttgg agtggtaagg cctgttttca gattaccata tgtacctctt 1020 cctcttgaaa agagggtaga gtttgtccga atcgttgaat ctattggacg ggaaaacttt 1080 gtgggtgaga acgaggcacg ggttcttgac gacgatgatt ttgtgttggt cagtaggtac 1140 taa 1143 30 380 PRT Oryza sativa 30 Met Ala Ser Leu Leu Ile Ala Ser Thr Gly Gly Ala His Arg Leu Ala 1 5 10 15 Trp Lys Asp Ala Ala Ala Leu Gly Pro Ala Pro Arg Leu Ala Arg Pro 20 25 30 Trp Pro Ala Ala Val Ala Ala Pro Ala Pro Leu Leu Arg Ile Ser Arg 35 40 45 Gly Lys Phe Ala Leu Gln Ala Ile Thr Leu Asp Asp Tyr Leu Pro Met 50 55 60 Arg Ser Thr Glu Val Lys Asn Arg Thr Ser Thr Ala Asp Ile Thr Ser 65 70 75 80 Leu Arg Val Ile Thr Ala Val Lys Thr Pro Tyr Leu Pro Asp Gly Arg 85 90 95 Phe Asp Leu Glu Ala Tyr Asp Ser Leu Ile Asn Met Gln Ile Asp Gly 100 105 110 Gly Ala Glu Gly Val Ile Val Gly Gly Thr Thr Gly Glu Gly His Leu 115 120 125 Met Ser Trp Asp Glu His Ile Met Leu Ile Gly His Thr Val Asn Cys 130 135 140 Phe Gly Ala Lys Val Lys Val Val Gly Asn Thr Gly Ser Asn Ser Thr 145 150 155 160 Arg Glu Ala Ile His Ala Thr Glu Gln Gly Phe Ala Val Gly Met His 165 170 175 Ala Ala Leu His Ile Asn Pro Tyr Tyr Gly Lys Thr Ser Ile Glu Gly 180 185 190 Leu Ile Ser His Phe Glu Ala Val Leu Pro Met Gly Pro Thr Ile Ile 195 200 205 Tyr Asn Val Pro Ser Arg Thr Gly Gln Asp Ile Pro Pro Ala Val Ile 210 215 220 Glu Ala Val Ser Ser Phe Thr Asn Leu Ala Gly Val Lys Glu Cys Val 225 230 235 240 Gly His Glu Arg Val Lys Cys Tyr Thr Asp Lys Gly Ile Thr Ile Trp 245 250 255 Ser Gly Asn Asp Asp Glu Cys His Asp Ser Arg Trp Lys Tyr Gly Ala 260 265 270 Thr Gly Val Ile Ser Val Ala Ser Asn Leu Ile Pro Gly Leu Met His 275 280 285 Asp Leu Met Tyr Glu Gly Glu Asn Lys Thr Leu Asn Glu Lys Leu Phe 290 295 300 Pro Leu Met Lys Trp Leu Phe Cys Gln Pro Asn Pro Ile Ala Leu Asn 305 310 315 320 Thr Ala Leu Ala Gln Leu Gly Val Val Arg Pro Val Phe Arg Leu Pro 325 330 335 Tyr Val Pro Leu Pro Leu Glu Lys Arg Val Glu Phe Val Arg Ile Val 340 345 350 Glu Ser Ile Gly Arg Glu Asn Phe Val Gly Glu Asn Glu Ala Arg Val 355 360 365 Leu Asp Asp Asp Asp Phe Val Leu Val Ser Arg Tyr 370 375 380 31 768 DNA Oryza sativa 31 atgcttcctc ctagggttgc cccctcctct ctggccgccg ccgccgccgc ggcgcctacc 60 tatctcgccg ccgcggcctc gacccctgct tccgtctggc tgcctgtgcc gcgtggagcc 120 ggagccgtgg cagtgtgcag ggccgccggg aaagggaagg aggtgctcag cggcgtggtc 180 ttccagccat tcgaggagct caagggggag ctctccctcg tcccccaggc caaggaccag 240 tctcttgcta ggcaaaagtt cgtcgacgag tgcgaggccg ccatcagcga gcagatcaat 300 gtggagttca atgcatcgta cgcgtaccac tcccttttcg cctactttga ccgtgacaac 360 gttgctctca agggattcgc caaattcttc aaagaatcca gcgatgagga gagggatcac 420 gcagagaaac tcatgaagta ccagaacatg cgtggaggca gggtgcggct ccagtccatc 480 gtcacaccct tgacagagtt cgaccatcct gagaaagggg atgccttgta tgctatggag 540 ttggccttgg ctctcgaaaa gcttgtaaat gagaagttgc acaacctgca cagtgtggca 600 tcaaggtgca atgatccaca gctgaccgac ttcgttgaga gtgaattcct tgaggagcag 660 gttgaagcca tcaagaagat ctctgagtat gtcgcccagc tgagaagagt gggaaagggg 720 catggggtgt ggcactttga tcagaagctg cttgaggaag aagcttga 768 32 255 PRT Oryza sativa 32 Met Leu Pro Pro Arg Val Ala Pro Ser Ser Leu Ala Ala Ala Ala Ala 1 5 10 15 Ala Ala Pro Thr Tyr Leu Ala Ala Ala Ala Ser Thr Pro Ala Ser Val 20 25 30 Trp Leu Pro Val Pro Arg Gly Ala Gly Ala Val Ala Val Cys Arg Ala 35 40 45 Ala Gly Lys Gly Lys Glu Val Leu Ser Gly Val Val Phe Gln Pro Phe 50 55 60 Glu Glu Leu Lys Gly Glu Leu Ser Leu Val Pro Gln Ala Lys Asp Gln 65 70 75 80 Ser Leu Ala Arg Gln Lys Phe Val Asp Glu Cys Glu Ala Ala Ile Ser 85 90 95 Glu Gln Ile Asn Val Glu Phe Asn Ala Ser Tyr Ala Tyr His Ser Leu 100 105 110 Phe Ala Tyr Phe Asp Arg Asp Asn Val Ala Leu Lys Gly Phe Ala Lys 115 120 125 Phe Phe Lys Glu Ser Ser Asp Glu Glu Arg Asp His Ala Glu Lys Leu 130 135 140 Met Lys Tyr Gln Asn Met Arg Gly Gly Arg Val Arg Leu Gln Ser Ile 145 150 155 160 Val Thr Pro Leu Thr Glu Phe Asp His Pro Glu Lys Gly Asp Ala Leu 165 170 175 Tyr Ala Met Glu Leu Ala Leu Ala Leu Glu Lys Leu Val Asn Glu Lys 180 185 190 Leu His Asn Leu His Ser Val Ala Ser Arg Cys Asn Asp Pro Gln Leu 195 200 205 Thr Asp Phe Val Glu Ser Glu Phe Leu Glu Glu Gln Val Glu Ala Ile 210 215 220 Lys Lys Ile Ser Glu Tyr Val Ala Gln Leu Arg Arg Val Gly Lys Gly 225 230 235 240 His Gly Val Trp His Phe Asp Gln Lys Leu Leu Glu Glu Glu Ala 245 250 255 33 756 DNA Oryza sativa 33 atgcttcctc ctagggttgc cccggccgcc gccgccgccg cgcctaccta tctcgccgcc 60 gcggcctcga cccctgcttc cgtctggctg cctgtgccgc gtggtgccgg acccggggca 120 gtgtgcaggg ccgccgggaa agggaaggag gtgctcagcg gcgtggtctt ccagccattc 180 gaggagctca agggggagct ctccctcgtc ccccaggcca aggaccagtc tctcgctagg 240 caaaagttcg tcgacgagtg cgaggccgcc atcaacgagc agatcaatgt ggagtacaat 300 gcatcgtacg cgtaccactc ccttttcgcc tactttgatc gtgacaacgt tgctctcaag 360 ggattcgcca aattcttcaa agaatccagc gatgaggaga gggatcacgc agagaaactc 420 atcaagtacc agaacatgcg tggaggcagg gtgcggctcc agtccatcgt cacacctttg 480 acagagttcg accatcctga gaaaggggat gccttgtatg ctatggagtt ggccttggct 540 ctcgaaaagc ttgtaaatga gaagttgcac aacctgcaca gtgtggcatc aaggtgcaat 600 gatccacagc tgaccgactt cgttgagagc gaattccttg aggagcaggt tgaagccatc 660 aagaagatct ctgagtatgt cgcccagctg agaagagtgg gaaaggggca tggggtgtgg 720 cactttgatc agaagctgct tgaggaagaa gcttga 756 34 251 PRT Oryza sativa 34 Met Leu Pro Pro Arg Val Ala Pro Ala Ala Ala Ala Ala Ala Pro Thr 1 5 10 15 Tyr Leu Ala Ala Ala Ala Ser Thr Pro Ala Ser Val Trp Leu Pro Val 20 25 30 Pro Arg Gly Ala Gly Pro Gly Ala Val Cys Arg Ala Ala Gly Lys Gly 35 40 45 Lys Glu Val Leu Ser Gly Val Val Phe Gln Pro Phe Glu Glu Leu Lys 50 55 60 Gly Glu Leu Ser Leu Val Pro Gln Ala Lys Asp Gln Ser Leu Ala Arg 65 70 75 80 Gln Lys Phe Val Asp Glu Cys Glu Ala Ala Ile Asn Glu Gln Ile Asn 85 90 95 Val Glu Tyr Asn Ala Ser Tyr Ala Tyr His Ser Leu Phe Ala Tyr Phe 100 105 110 Asp Arg Asp Asn Val Ala Leu Lys Gly Phe Ala Lys Phe Phe Lys Glu 115 120 125 Ser Ser Asp Glu Glu Arg Asp His Ala Glu Lys Leu Ile Lys Tyr Gln 130 135 140 Asn Met Arg Gly Gly Arg Val Arg Leu Gln Ser Ile Val Thr Pro Leu 145 150 155 160 Thr Glu Phe Asp His Pro Glu Lys Gly Asp Ala Leu Tyr Ala Met Glu 165 170 175 Leu Ala Leu Ala Leu Glu Lys Leu Val Asn Glu Lys Leu His Asn Leu 180 185 190 His Ser Val Ala Ser Arg Cys Asn Asp Pro Gln Leu Thr Asp Phe Val 195 200 205 Glu Ser Glu Phe Leu Glu Glu Gln Val Glu Ala Ile Lys Lys Ile Ser 210 215 220 Glu Tyr Val Ala Gln Leu Arg Arg Val Gly Lys Gly His Gly Val Trp 225 230 235 240 His Phe Asp Gln Lys Leu Leu Glu Glu Glu Ala 245 250 35 1662 DNA Oryza sativa 35 atgtatcggg tgaagagcga gagcgactgc gatatgatcc atcaggagca gatggactcg 60 ccggtggccg acgacggcag cagcgggggg tcgccgcacc gcggcggcgg gcccccgctg 120 aagaaggggc catggacgtc ggcggaggac gccatcctgg tggactacgt gaagaagcac 180 ggcgagggga actggaacgc ggtgcagaag aacaccgggc tgttccggtg cggcaagagc 240 tgccgcctcc ggtgggcgaa ccacctgagg cccaacctca agaagggggc cttcaccgcc 300 gaggaggaga ggctcatcat ccagctccac tccaagatgg ggaacaagtg ggctcggatg 360 gccgctcatt tgccagggcg cactgataat gaaataaaga attactggaa tactcgaata 420 aagagatgcc agcgagctgg cctacccatc tatcctacca gcgtatgcaa tcaatcctca 480 aatgaagatc agcagtgctc cagtgatttt gactgtggcg agaatttgtc aaacgatctt 540 ctgaatgcaa atggtcttta cctaccagat tttacctgtg acaatttcat tgctaattca 600 gaggctttac cttatgcacc acatctttca gccgtttcta taagcaatct ccttggccag 660 agctttgcat caaaaagctg tagcttcatg gatcaggtaa accagacagg gatgctaaaa 720 cagtctgatg gtgtgcttcc tggattgagc gataccatca acggtgtgat ttcctcggtg 780 gatcaattct caaatgactc tgagaagctc aagcaggctg tgggttttga ctatctccat 840 gaagccaact ctaccagcaa gattattgca cctttcgggg gtgcacttaa tggcagccat 900 gcctttttaa atggcaattt ctctgcttct aggcccacaa gtggtccttt gaagatggag 960 ctcccttcac tccaagatac tgaatctgat ccaaacagct ggctcaagta cactgtagct 1020 cctgcgttgc agcctactga gttagttgat ccctacctgc agtctccagc agcaacccct 1080 tcagtgaaat cagagtgcgc gtcgccaagg aatagtggcc ttttggaaga gttgattcat 1140 gaagctcgga ccctaagatc cgggaagaac caacagacat ctgtgataag ttctagttct 1200 tctgtcggta cgccatgtaa tactacggtt cttagcccag agtttgatat gtgtcaggaa 1260 tactggggag aacaacatcc tggtccattc ctcaatgact gtgctccttt cagtggcaat 1320 tcattcactg aatccacccc tcctgttagc gctgcatcgc ctgacatctt tcagctctcc 1380 aaagtttccc cagcacaaag cacttcaatg ggatctggag agcaagtaat ggggcctaaa 1440 tatgaacctg gggacacttc acctcatcct gaaaacttca ggccagatgc attgttttct 1500 gggaatacag ctgatccatc agttttcaac aatgccatag caatgcttct gggcaatgac 1560 ttgagtatcg attgcagacc tgttcttggc gacggtatca tgttcaattc ttcctcgtgg 1620 agcaacatgc cacacgcctg tgaaatgtca gaattcaaat ga 1662 36 553 PRT Oryza sativa 36 Met Tyr Arg Val Lys Ser Glu Ser Asp Cys Asp Met Ile His Gln Glu 1 5 10 15 Gln Met Asp Ser Pro Val Ala Asp Asp Gly Ser Ser Gly Gly Ser Pro 20 25 30 His Arg Gly Gly Gly Pro Pro Leu Lys Lys Gly Pro Trp Thr Ser Ala 35 40 45 Glu Asp Ala Ile Leu Val Asp Tyr Val Lys Lys His Gly Glu Gly Asn 50 55 60 Trp Asn Ala Val Gln Lys Asn Thr Gly Leu Phe Arg Cys Gly Lys Ser 65 70 75 80 Cys Arg Leu Arg Trp Ala Asn His Leu Arg Pro Asn Leu Lys Lys Gly 85 90 95 Ala Phe Thr Ala Glu Glu Glu Arg Leu Ile Ile Gln Leu His Ser Lys 100 105 110 Met Gly Asn Lys Trp Ala Arg Met Ala Ala His Leu Pro Gly Arg Thr 115 120 125 Asp Asn Glu Ile Lys Asn Tyr Trp Asn Thr Arg Ile Lys Arg Cys Gln 130 135 140 Arg Ala Gly Leu Pro Ile Tyr Pro Thr Ser Val Cys Asn Gln Ser Ser 145 150 155 160 Asn Glu Asp Gln Gln Cys Ser Ser Asp Phe Asp Cys Gly Glu Asn Leu 165 170 175 Ser Asn Asp Leu Leu Asn Ala Asn Gly Leu Tyr Leu Pro Asp Phe Thr 180 185 190 Cys Asp Asn Phe Ile Ala Asn Ser Glu Ala Leu Pro Tyr Ala Pro His 195 200 205 Leu Ser Ala Val Ser Ile Ser Asn Leu Leu Gly Gln Ser Phe Ala Ser 210 215 220 Lys Ser Cys Ser Phe Met Asp Gln Val Asn Gln Thr Gly Met Leu Lys 225 230 235 240 Gln Ser Asp Gly Val Leu Pro Gly Leu Ser Asp Thr Ile Asn Gly Val 245 250 255 Ile Ser Ser Val Asp Gln Phe Ser Asn Asp Ser Glu Lys Leu Lys Gln 260 265 270 Ala Val Gly Phe Asp Tyr Leu His Glu Ala Asn Ser Thr Ser Lys Ile 275 280 285 Ile Ala Pro Phe Gly Gly Ala Leu Asn Gly Ser His Ala Phe Leu Asn 290 295 300 Gly Asn Phe Ser Ala Ser Arg Pro Thr Ser Gly Pro Leu Lys Met Glu 305 310 315 320 Leu Pro Ser Leu Gln Asp Thr Glu Ser Asp Pro Asn Ser Trp Leu Lys 325 330 335 Tyr Thr Val Ala Pro Ala Leu Gln Pro Thr Glu Leu Val Asp Pro Tyr 340 345 350 Leu Gln Ser Pro Ala Ala Thr Pro Ser Val Lys Ser Glu Cys Ala Ser 355 360 365 Pro Arg Asn Ser Gly Leu Leu Glu Glu Leu Ile His Glu Ala Arg Thr 370 375 380 Leu Arg Ser Gly Lys Asn Gln Gln Thr Ser Val Ile Ser Ser Ser Ser 385 390 395 400 Ser Val Gly Thr Pro Cys Asn Thr Thr Val Leu Ser Pro Glu Phe Asp 405 410 415 Met Cys Gln Glu Tyr Trp Gly Glu Gln His Pro Gly Pro Phe Leu Asn 420 425 430 Asp Cys Ala Pro Phe Ser Gly Asn Ser Phe Thr Glu Ser Thr Pro Pro 435 440 445 Val Ser Ala Ala Ser Pro Asp Ile Phe Gln Leu Ser Lys Val Ser Pro 450 455 460 Ala Gln Ser Thr Ser Met Gly Ser Gly Glu Gln Val Met Gly Pro Lys 465 470 475 480 Tyr Glu Pro Gly Asp Thr Ser Pro His Pro Glu Asn Phe Arg Pro Asp 485 490 495 Ala Leu Phe Ser Gly Asn Thr Ala Asp Pro Ser Val Phe Asn Asn Ala 500 505 510 Ile Ala Met Leu Leu Gly Asn Asp Leu Ser Ile Asp Cys Arg Pro Val 515 520 525 Leu Gly Asp Gly Ile Met Phe Asn Ser Ser Ser Trp Ser Asn Met Pro 530 535 540 His Ala Cys Glu Met Ser Glu Phe Lys 545 550 37 1089 DNA Oryza sativa 37 atggcccacg ccgccgcggc cacgggcgca ctggcaccgc tgcatccact gctccgctgc 60 acgagccgtc atctctgcgc ctcggcttcc cctcgcgccg gcctctgcct ccaccaccac 120 cgccgccgcc gccgcagcag ccggaggacg aaactcgccg tgcgcgcgat ggcaccgacg 180 ttgtcctcgt cgtcgacggc ggcggcagct cccccggggc tgaaggaggg catcgcgggg 240 ctctacgacg agtcgtccgg cgtgtgggag agcatctggg gcgagcacat gcaccacggc 300 ttctacgacg ccggcgaggc cgcctccatg tccgaccacc gccgcgccca gatccgcatg 360 atcgaggaat ccctcgcctt cgccgccgtc cccgatgatg cggagaagaa acccaaaagt 420 gtagttgatg ttggctgtgg cattggtggt agctcaagat acttggcgaa caaatacgga 480 gcgcaatgct acggcatcac gttgagtccg gtgcaggctg aaagaggaaa tgccctcgcg 540 gcagagcaag ggttatcaga caaggtctcc tttcaagttg gtgatgcatt ggagcagcct 600 tttcctgatg ggcagtttga tcttgtctgg tccatggaga gtggcgagca catgccagac 660 aaacggcagt ttgtaagcga gctggcacgc gtcgcagctc ctggggcgag aataatcatt 720 gtgacctggt gccataggaa cctcgagcca tccgaagagt ccctgaaacc tgatgagctg 780 aatctcctga aaaggatatg cgatgcatat tatctcccag actggtgctc tccttctgat 840 tatgtcaaaa ttgccgagtc actgtctctt gaggatataa ggacagctga ttggtcagag 900 aacgtcgccc cattctggcc tgcggttata aaatcagcat tgacatggaa aggtttaact 960 tctctgctaa gaagtgggtg gaagacgata agaggtgcaa tggtgatgcc tctgatgatc 1020 gaaggataca agaaagggct catcaaattc accatcatca cctgtcgcaa gcccgaaaca 1080 acgcagtag 1089 38 362 PRT Oryza sativa 38 Met Ala His Ala Ala Ala Ala Thr Gly Ala Leu Ala Pro Leu His Pro 1 5 10 15 Leu Leu Arg Cys Thr Ser Arg His Leu Cys Ala Ser Ala Ser Pro Arg 20 25 30 Ala Gly Leu Cys Leu His His His Arg Arg Arg Arg Arg Ser Ser Arg 35 40 45 Arg Thr Lys Leu Ala Val Arg Ala Met Ala Pro Thr Leu Ser Ser Ser 50 55 60 Ser Thr Ala Ala Ala Ala Pro Pro Gly Leu Lys Glu Gly Ile Ala Gly 65 70 75 80 Leu Tyr Asp Glu Ser Ser Gly Val Trp Glu Ser Ile Trp Gly Glu His 85 90 95 Met His His Gly Phe Tyr Asp Ala Gly Glu Ala Ala Ser Met Ser Asp 100 105 110 His Arg Arg Ala Gln Ile Arg Met Ile Glu Glu Ser Leu Ala Phe Ala 115 120 125 Ala Val Pro Asp Asp Ala Glu Lys Lys Pro Lys Ser Val Val Asp Val 130 135 140 Gly Cys Gly Ile Gly Gly Ser Ser Arg Tyr Leu Ala Asn Lys Tyr Gly 145 150 155 160 Ala Gln Cys Tyr Gly Ile Thr Leu Ser Pro Val Gln Ala Glu Arg Gly 165 170 175 Asn Ala Leu Ala Ala Glu Gln Gly Leu Ser Asp Lys Val Ser Phe Gln 180 185 190 Val Gly Asp Ala Leu Glu Gln Pro Phe Pro Asp Gly Gln Phe Asp Leu 195 200 205 Val Trp Ser Met Glu Ser Gly Glu His Met Pro Asp Lys Arg Gln Phe 210 215 220 Val Ser Glu Leu Ala Arg Val Ala Ala Pro Gly Ala Arg Ile Ile Ile 225 230 235 240 Val Thr Trp Cys His Arg Asn Leu Glu Pro Ser Glu Glu Ser Leu Lys 245 250 255 Pro Asp Glu Leu Asn Leu Leu Lys Arg Ile Cys Asp Ala Tyr Tyr Leu 260 265 270 Pro Asp Trp Cys Ser Pro Ser Asp Tyr Val Lys Ile Ala Glu Ser Leu 275 280 285 Ser Leu Glu Asp Ile Arg Thr Ala Asp Trp Ser Glu Asn Val Ala Pro 290 295 300 Phe Trp Pro Ala Val Ile Lys Ser Ala Leu Thr Trp Lys Gly Leu Thr 305 310 315 320 Ser Leu Leu Arg Ser Gly Trp Lys Thr Ile Arg Gly Ala Met Val Met 325 330 335 Pro Leu Met Ile Glu Gly Tyr Lys Lys Gly Leu Ile Lys Phe Thr Ile 340 345 350 Ile Thr Cys Arg Lys Pro Glu Thr Thr Gln 355 360 39 1161 DNA Oryza sativa 39 atggcttgct ccacccacct cctgtcccag agcctctacc cgctcaaccg cgctaacccg 60 gcagccgcgc gcgggcacct ccggttccag gcttctccca gtgtgaggct cggctccggc 120 accagtcgcc gccgggcgct gggcctgaga gtcgccgcgt cggcggagca agggaggagg 180 caagtggagg ttgagtatga tctacaagca aagttcaaca agctagcgga ccaaattgac 240 cagaatgctg ggattacacg gctgaaccta ttctcacctt gcaaaattaa tgtgttcttg 300 aggataacgg gtaagagacc agatgggttc catgacctgg cttctctgtt tcatgtgata 360 agtttgggtg atactatcaa attctcattg tcaccaagta agagcaaaga tcgcttgtca 420 accaatgtag caggtgtccc agttgatgaa agcaatttga tcatcaaggc actcaatctt 480 taccgcaaga aaactggaac tgacaacttt ttttggattc atcttgataa gaaggtccct 540 actggtgctg gtcttggtgg tggaagcagt aatgctgcaa ctgcgctgtg ggccgccaac 600 cagtttagtg gctgcattgc ttcagaaaag gagcttcagg agtggtctgg agagatagga 660 tcggatattc ccttcttctt ttcacaagga gcagcgtatt gtaccggtag aggagagatt 720 gttgaagata ttcggaatcc attgccagca aatttgccga tggtactagt aaagccacct 780 gaagcatgct caacagctga agtttacaag cggctcaggt tagagcacac aagtcaaact 840 gatcccttgg tattgctcaa ggaaattact gaaaatggga tatcacagga tgcctgtgtt 900 aatgatctag aacctccagc atttgaggtg ttgccatcac taaagaggtt gaagaaacgt 960 ataattgctg ctaaccgggg agattatgat gctgttttta tgtcaggaag tggaagcaca 1020 attgttggga ttggttcacc agatccgcct gcatttgtgt atgatgatga tgactacaag 1080 gatacttttg tgtcagaggc ctgcttcctc actcgtaatg agaacgagtg gtacagaacc 1140 aatctcatcg aaaatcacta g 1161 40 386 PRT Oryza sativa 40 Met Ala Cys Ser Thr His Leu Leu Ser Gln Ser Leu Tyr Pro Leu Asn 1 5 10 15 Arg Ala Asn Pro Ala Ala Ala Arg Gly His Leu Arg Phe Gln Ala Ser 20 25 30 Pro Ser Val Arg Leu Gly Ser Gly Thr Ser Arg Arg Arg Ala Leu Gly 35 40 45 Leu Arg Val Ala Ala Ser Ala Glu Gln Gly Arg Arg Gln Val Glu Val 50 55 60 Glu Tyr Asp Leu Gln Ala Lys Phe Asn Lys Leu Ala Asp Gln Ile Asp 65 70 75 80 Gln Asn Ala Gly Ile Thr Arg Leu Asn Leu Phe Ser Pro Cys Lys Ile 85 90 95 Asn Val Phe Leu Arg Ile Thr Gly Lys Arg Pro Asp Gly Phe His Asp 100 105 110 Leu Ala Ser Leu Phe His Val Ile Ser Leu Gly Asp Thr Ile Lys Phe 115 120 125 Ser Leu Ser Pro Ser Lys Ser Lys Asp Arg Leu Ser Thr Asn Val Ala 130 135 140 Gly Val Pro Val Asp Glu Ser Asn Leu Ile Ile Lys Ala Leu Asn Leu 145 150 155 160 Tyr Arg Lys Lys Thr Gly Thr Asp Asn Phe Phe Trp Ile His Leu Asp 165 170 175 Lys Lys Val Pro Thr Gly Ala Gly Leu Gly Gly Gly Ser Ser Asn Ala 180 185 190 Ala Thr Ala Leu Trp Ala Ala Asn Gln Phe Ser Gly Cys Ile Ala Ser 195 200 205 Glu Lys Glu Leu Gln Glu Trp Ser Gly Glu Ile Gly Ser Asp Ile Pro 210 215 220 Phe Phe Phe Ser Gln Gly Ala Ala Tyr Cys Thr Gly Arg Gly Glu Ile 225 230 235 240 Val Glu Asp Ile Arg Asn Pro Leu Pro Ala Asn Leu Pro Met Val Leu 245 250 255 Val Lys Pro Pro Glu Ala Cys Ser Thr Ala Glu Val Tyr Lys Arg Leu 260 265 270 Arg Leu Glu His Thr Ser Gln Thr Asp Pro Leu Val Leu Leu Lys Glu 275 280 285 Ile Thr Glu Asn Gly Ile Ser Gln Asp Ala Cys Val Asn Asp Leu Glu 290 295 300 Pro Pro Ala Phe Glu Val Leu Pro Ser Leu Lys Arg Leu Lys Lys Arg 305 310 315 320 Ile Ile Ala Ala Asn Arg Gly Asp Tyr Asp Ala Val Phe Met Ser Gly 325 330 335 Ser Gly Ser Thr Ile Val Gly Ile Gly Ser Pro Asp Pro Pro Ala Phe 340 345 350 Val Tyr Asp Asp Asp Asp Tyr Lys Asp Thr Phe Val Ser Glu Ala Cys 355 360 365 Phe Leu Thr Arg Asn Glu Asn Glu Trp Tyr Arg Thr Asn Leu Ile Glu 370 375 380 Asn His 385 41 1278 DNA Oryza sativa 41 atggagcggg tgttctccgt ggaggagatc tccgacccat tctgggtccc gcctccgccg 60 ccgcagtcgg cggcggcggc ccagcagcag ggcggcggcg gcgtggcttc gggaggtggt 120 ggtggtgtag cggggggcgg cggcggcggg aacgcgatga accggtgccc gtcggagtgg 180 tacttccaga agtttctgga ggaggcggtg ctcgatagcc ccgtcccgaa ccctagcccg 240 agggccgaag cgggagggat caggggcgca ggaggggtgg tgccggtcga tgttaagcag 300 ccgcagctct cggcggcggc ggcggcggcg gcgacgacga gcgcggtggt ggaccccgtg 360 gagtacaacg cgatgctgaa gcagaagctg gagaaggacc tcgccgcggt cgccatgtgg 420 agggcctctg gcacagttcc acctgagcgt cctggagctg gttcatcctt gctgaatgca 480 gatgtttcac acataggcgc tcctaattcc atcggaggca atgctactcc agttcaaaac 540 atgctaagtg gcccaagtgg gggatcgggc tcacagttgg tacagaatgt tgatgtcctt 600 gtaaagcagc ccaccagctc ttcatcaagg gagcagtcag atgatgatga catggaggga 660 gaagctgaga ccactggaac tgcaagacct gctgatcaaa gattacaacg aaggaagcaa 720 tccaatcggg agtcagccag gcgctcaaga agcagaaagg cagctcactt gaatgagctg 780 gaggcacagg tatcgcaatt aagagtcgag aactcctcgc tgttaaggcg tcttgctgat 840 gttaaccaga agtacaatga tgctgctgtt gacaatagag tgctaaaagc agatgttgag 900 accttgagag caaaggtgaa gatggcagag gactcggtga agcgggtgac aggcatgaac 960 gcgttgtttc ccgccgcttc tgatatgtca tccctcagca tgccattcaa cagctcccca 1020 tctgaagcaa cgtcagacgc tgctgttccc atccaagatg acccgaacaa ttacttcgct 1080 actaacaacg acatcggagg taacaacaac tacatgcccg acataccttc ttcggctcag 1140 gaggacgagg acttcgtcaa tggcgctctg gctgccggca agattggccg gacagcctcg 1200 ctgcagcggg tggcgagcct ggagcatctc cagaagagga tgtgcggtgg gccggcttcg 1260 tctgggtcga cgtcctga 1278 42 425 PRT Oryza sativa 42 Met Glu Arg Val Phe Ser Val Glu Glu Ile Ser Asp Pro Phe Trp Val 1 5 10 15 Pro Pro Pro Pro Pro Gln Ser Ala Ala Ala Ala Gln Gln Gln Gly Gly 20 25 30 Gly Gly Val Ala Ser Gly Gly Gly Gly Gly Val Ala Gly Gly Gly Gly 35 40 45 Gly Gly Asn Ala Met Asn Arg Cys Pro Ser Glu Trp Tyr Phe Gln Lys 50 55 60 Phe Leu Glu Glu Ala Val Leu Asp Ser Pro Val Pro Asn Pro Ser Pro 65 70 75 80 Arg Ala Glu Ala Gly Gly Ile Arg Gly Ala Gly Gly Val Val Pro Val 85 90 95 Asp Val Lys Gln Pro Gln Leu Ser Ala Ala Ala Ala Ala Ala Ala Thr 100 105 110 Thr Ser Ala Val Val Asp Pro Val Glu Tyr Asn Ala Met Leu Lys Gln 115 120 125 Lys Leu Glu Lys Asp Leu Ala Ala Val Ala Met Trp Arg Ala Ser Gly 130 135 140 Thr Val Pro Pro Glu Arg Pro Gly Ala Gly Ser Ser Leu Leu Asn Ala 145 150 155 160 Asp Val Ser His Ile Gly Ala Pro Asn Ser Ile Gly Gly Asn Ala Thr 165 170 175 Pro Val Gln Asn Met Leu Ser Gly Pro Ser Gly Gly Ser Gly Ser Gln 180 185 190 Leu Val Gln Asn Val Asp Val Leu Val Lys Gln Pro Thr Ser Ser Ser 195 200 205 Ser Arg Glu Gln Ser Asp Asp Asp Asp Met Glu Gly Glu Ala Glu Thr 210 215 220 Thr Gly Thr Ala Arg Pro Ala Asp Gln Arg Leu Gln Arg Arg Lys Gln 225 230 235 240 Ser Asn Arg Glu Ser Ala Arg Arg Ser Arg Ser Arg Lys Ala Ala His 245 250 255 Leu Asn Glu Leu Glu Ala Gln Val Ser Gln Leu Arg Val Glu Asn Ser 260 265 270 Ser Leu Leu Arg Arg Leu Ala Asp Val Asn Gln Lys Tyr Asn Asp Ala 275 280 285 Ala Val Asp Asn Arg Val Leu Lys Ala Asp Val Glu Thr Leu Arg Ala 290 295 300 Lys Val Lys Met Ala Glu Asp Ser Val Lys Arg Val Thr Gly Met Asn 305 310 315 320 Ala Leu Phe Pro Ala Ala Ser Asp Met Ser Ser Leu Ser Met Pro Phe 325 330 335 Asn Ser Ser Pro Ser Glu Ala Thr Ser Asp Ala Ala Val Pro Ile Gln 340 345 350 Asp Asp Pro Asn Asn Tyr Phe Ala Thr Asn Asn Asp Ile Gly Gly Asn 355 360 365 Asn Asn Tyr Met Pro Asp Ile Pro Ser Ser Ala Gln Glu Asp Glu Asp 370 375 380 Phe Val Asn Gly Ala Leu Ala Ala Gly Lys Ile Gly Arg Thr Ala Ser 385 390 395 400 Leu Gln Arg Val Ala Ser Leu Glu His Leu Gln Lys Arg Met Cys Gly 405 410 415 Gly Pro Ala Ser Ser Gly Ser Thr Ser 420 425 43 831 DNA Oryza sativa 43 atgacgggca gtagttgtcc ggccgattct tcccagctgc tgtaccctcg ccggggtgcc 60 cccaccacca ccaccacctc ccgtcctcct ctccatccgc tcatcgctca tgcgccctac 120 gacgtcgtcc tccaccgatc tgtcgtcctc tccatcagct cagctcgtga tcaggctgag 180 ctcgcgagct tctggtgcta tataaggctg ggtggtggtg caagtgcgaa gcgagcggcc 240 ggtgaggacg atcgatcgag atcgagcttg acggcggcga gaggaggagg aggggagacg 300 atgagcgggc gggggagggg ggacccgctg gtgctgggga gggtggtggg ggacgtggtg 360 gacccgttcg tgaggagggt ggcgctgcgg gtggcgtacg gagcgcggga ggtggccaac 420 ggctgcgagc tccgcccctc cgccgtcgcc gaccagcccc gcgtcgccgt cggcggcccc 480 gacatgcgca ccttctacac cctggtgatg gtggatccgg acgcgccgag cccgagcgat 540 ccaaacctca gggagtacct gcactggctg gtcaccggca tcccggctac cacaggagtc 600 tcttttggga cagaggtggt gtgctacgag agcccgcggc cggtgctggg gatccacagg 660 ctggtgttcc tgctgttcga gcagctgggg cggcagacgg tgtacgcacc ggggtggcgc 720 cagaacttca gcacccgcga cttcgccgag ctctacaacc tcggcctccc tgtcgccgcc 780 gtctacttca actgccagag ggagtctgga accgaaggaa aaagaatgtg a 831 44 276 PRT Oryza sativa 44 Met Thr Gly Ser Ser Cys Pro Ala Asp Ser Ser Gln Leu Leu Tyr Pro 1 5 10 15 Arg Arg Gly Ala Pro Thr Thr Thr Thr Thr Ser Arg Pro Pro Leu His 20 25 30 Pro Leu Ile Ala His Ala Pro Tyr Asp Val Val Leu His Arg Ser Val 35 40 45 Val Leu Ser Ile Ser Ser Ala Arg Asp Gln Ala Glu Leu Ala Ser Phe 50 55 60 Trp Cys Tyr Ile Arg Leu Gly Gly Gly Ala Ser Ala Lys Arg Ala Ala 65 70 75 80 Gly Glu Asp Asp Arg Ser Arg Ser Ser Leu Thr Ala Ala Arg Gly Gly 85 90 95 Gly Gly Glu Thr Met Ser Gly Arg Gly Arg Gly Asp Pro Leu Val Leu 100 105 110 Gly Arg Val Val Gly Asp Val Val Asp Pro Phe Val Arg Arg Val Ala 115 120 125 Leu Arg Val Ala Tyr Gly Ala Arg Glu Val Ala Asn Gly Cys Glu Leu 130 135 140 Arg Pro Ser Ala Val Ala Asp Gln Pro Arg Val Ala Val Gly Gly Pro 145 150 155 160 Asp Met Arg Thr Phe Tyr Thr Leu Val Met Val Asp Pro Asp Ala Pro 165 170 175 Ser Pro Ser Asp Pro Asn Leu Arg Glu Tyr Leu His Trp Leu Val Thr 180 185 190 Gly Ile Pro Ala Thr Thr Gly Val Ser Phe Gly Thr Glu Val Val Cys 195 200 205 Tyr Glu Ser Pro Arg Pro Val Leu Gly Ile His Arg Leu Val Phe Leu 210 215 220 Leu Phe Glu Gln Leu Gly Arg Gln Thr Val Tyr Ala Pro Gly Trp Arg 225 230 235 240 Gln Asn Phe Ser Thr Arg Asp Phe Ala Glu Leu Tyr Asn Leu Gly Leu 245 250 255 Pro Val Ala Ala Val Tyr Phe Asn Cys Gln Arg Glu Ser Gly Thr Glu 260 265 270 Gly Lys Arg Met 275 45 630 DNA Oryza sativa 45 atgggccaac ttcttggcaa gaagtacata taccttgggc tctttgacac cgaagttgaa 60 gctgcaagag catatgacag ggcagctatt cgcttcaatg ggagggaagc tgttaccaac 120 ttcgagcctg catcctacaa tgtggatgct ttaccagacg ccggaaatga ggcaattgtt 180 gatggcgatc ttgatttgga tttgcggatt tcgcaaccta atgcgcgtga ctccaaaagc 240 gatgtcgcca caactggcct ccagttaact tgtgattccc ctgaatcttc aaatattaca 300 gtccaccagc caatgggctc gtctccccaa tggactgtgc atcaccaaag cacaccactg 360 ccccctcagc atcaacgttt gtacccatct cattgtcttg gcttcctccc gaacctacag 420 gagaggccaa tggacagaag gcctgagctg ggtcccatgc cgttcccaac acaggcttgg 480 caaatgcagg ccccttctca cttgccattg ctccacgctg cagcatcatc aggattctct 540 gccggcgccg gcgccggcgt cgccgccgcc acccgccggc agccgccgtt cccggcggat 600 caccccttct acttcccgcc aaccgcctga 630 46 209 PRT Oryza sativa 46 Met Gly Gln Leu Leu Gly Lys Lys Tyr Ile Tyr Leu Gly Leu Phe Asp 1 5 10 15 Thr Glu Val Glu Ala Ala Arg Ala Tyr Asp Arg Ala Ala Ile Arg Phe 20 25 30 Asn Gly Arg Glu Ala Val Thr Asn Phe Glu Pro Ala Ser Tyr Asn Val 35 40 45 Asp Ala Leu Pro Asp Ala Gly Asn Glu Ala Ile Val Asp Gly Asp Leu 50 55 60 Asp Leu Asp Leu Arg Ile Ser Gln Pro Asn Ala Arg Asp Ser Lys Ser 65 70 75 80 Asp Val Ala Thr Thr Gly Leu Gln Leu Thr Cys Asp Ser Pro Glu Ser 85 90 95 Ser Asn Ile Thr Val His Gln Pro Met Gly Ser Ser Pro Gln Trp Thr 100 105 110 Val His His Gln Ser Thr Pro Leu Pro Pro Gln His Gln Arg Leu Tyr 115 120 125 Pro Ser His Cys Leu Gly Phe Leu Pro Asn Leu Gln Glu Arg Pro Met 130 135 140 Asp Arg Arg Pro Glu Leu Gly Pro Met Pro Phe Pro Thr Gln Ala Trp 145 150 155 160 Gln Met Gln Ala Pro Ser His Leu Pro Leu Leu His Ala Ala Ala Ser 165 170 175 Ser Gly Phe Ser Ala Gly Ala Gly Ala Gly Val Ala Ala Ala Thr Arg 180 185 190 Arg Gln Pro Pro Phe Pro Ala Asp His Pro Phe Tyr Phe Pro Pro Thr 195 200 205 Ala 47 1110 DNA Oryza sativa 47 atggagaagt tgctttcctc ctccggcgcc gccgccgccg tggcgtcgca gggccagctc 60 ccggactgct tcgtgttccc ggccgaccgg cgcccaccgg cctccaccgc ggccgtgtcg 120 ctccccgtca tcgacctctc cggcccccgc gacgccgtcc gccgcgccgt cctcgacgcc 180 ggcaaggagc tcggcttctt ccaggtcaga aaacaacaga atccccaagc ctgtaggtat 240 acacacagct tctctctcaa tcgcttgaca tggcggtgcc gtgcgtgcaa ggtggtgaac 300 cacggcgtgc cgccggagac gatgcgggag atggcggcgg tgtgcgagga gttcttccgg 360 ctgccggcgg aggacaaggc ggcgttctac tccgacgcgg aggagaaccc caaccgcctc 420 ttctccagca ccatctacga ggtcggcgac cagcgctact ggcgcgactg cctccgcctc 480 gcctgcggct tccccgtcgc cgacgacacc aacacccact ggcccgacaa gccccaccat 540 ctccgggatg tcacggagaa gttcttcgtg gcgacgaggg gattggggat cgagctgctg 600 cggctgctgt gcgaggggat ggggctcagg ccggactact tcgagcgcga cctcaccgcc 660 ggcgatgtca tcatcaacgt caaccactac cctccatgcc cggatccgag cctgacgctg 720 ggcttgccgc cgcactgcga ccgcaacctc atcaccctgc tcctccaggg cgacgtcttc 780 ggcctccagg tctcctacaa tggcgactgg atcaacgtcg accccgtccc cgacgccttc 840 gtcgtcaact ttggccacct cctcgagatt gcgacgaacg gagtgctgaa gagcattgag 900 cacagggcga tgacgaactc ggcggtggcg aggacgtcgg tggcgacgtt catgatgccg 960 ccgatggact gcctcgtcgg accggcgaag gagctcgtcg gagacggcgg ccagccgcag 1020 tatcgcaccg tcacgttccg cgagttcatg cgcatctaca agaccgtcgg cgcgcgccgc 1080 gacagcgtcg agaaggcctt caaaatctga 1110 48 369 PRT Oryza sativa 48 Met Glu Lys Leu Leu Ser Ser Ser Gly Ala Ala Ala Ala Val Ala Ser 1 5 10 15 Gln Gly Gln Leu Pro Asp Cys Phe Val Phe Pro Ala Asp Arg Arg Pro 20 25 30 Pro Ala Ser Thr Ala Ala Val Ser Leu Pro Val Ile Asp Leu Ser Gly 35 40 45 Pro Arg Asp Ala Val Arg Arg Ala Val Leu Asp Ala Gly Lys Glu Leu 50 55 60 Gly Phe Phe Gln Val Arg Lys Gln Gln Asn Pro Gln Ala Cys Arg Tyr 65 70 75 80 Thr His Ser Phe Ser Leu Asn Arg Leu Thr Trp Arg Cys Arg Ala Cys 85 90 95 Lys Val Val Asn His Gly Val Pro Pro Glu Thr Met Arg Glu Met Ala 100 105 110 Ala Val Cys Glu Glu Phe Phe Arg Leu Pro Ala Glu Asp Lys Ala Ala 115 120 125 Phe Tyr Ser Asp Ala Glu Glu Asn Pro Asn Arg Leu Phe Ser Ser Thr 130 135 140 Ile Tyr Glu Val Gly Asp Gln Arg Tyr Trp Arg Asp Cys Leu Arg Leu 145 150 155 160 Ala Cys Gly Phe Pro Val Ala Asp Asp Thr Asn Thr His Trp Pro Asp 165 170 175 Lys Pro His His Leu Arg Asp Val Thr Glu Lys Phe Phe Val Ala Thr 180 185 190 Arg Gly Leu Gly Ile Glu Leu Leu Arg Leu Leu Cys Glu Gly Met Gly 195 200 205 Leu Arg Pro Asp Tyr Phe Glu Arg Asp Leu Thr Ala Gly Asp Val Ile 210 215 220 Ile Asn Val Asn His Tyr Pro Pro Cys Pro Asp Pro Ser Leu Thr Leu 225 230 235 240 Gly Leu Pro Pro His Cys Asp Arg Asn Leu Ile Thr Leu Leu Leu Gln 245 250 255 Gly Asp Val Phe Gly Leu Gln Val Ser Tyr Asn Gly Asp Trp Ile Asn 260 265 270 Val Asp Pro Val Pro Asp Ala Phe Val Val Asn Phe Gly His Leu Leu 275 280 285 Glu Ile Ala Thr Asn Gly Val Leu Lys Ser Ile Glu His Arg Ala Met 290 295 300 Thr Asn Ser Ala Val Ala Arg Thr Ser Val Ala Thr Phe Met Met Pro 305 310 315 320 Pro Met Asp Cys Leu Val Gly Pro Ala Lys Glu Leu Val Gly Asp Gly 325 330 335 Gly Gln Pro Gln Tyr Arg Thr Val Thr Phe Arg Glu Phe Met Arg Ile 340 345 350 Tyr Lys Thr Val Gly Ala Arg Arg Asp Ser Val Glu Lys Ala Phe Lys 355 360 365 Ile 49 1023 DNA Oryza sativa 49 atggagaagt tgctttcctc ctccggcgcc gccgccgccg tggcgtcgca gggccagctc 60 ccggactgct tcgtgttccc ggccgaccgg cgcccaccgg cctccaccgc ggccgtgtcg 120 ctccccgtca tcgacctctc cggcccccgc gacgccgtcc gccgcgccgt cctcgacgcc 180 ggcaaggagc tcggcttctt ccaggtggtg aaccacggcg tgccgccgga gacgatgcgg 240 gagatggcgg cggtgtgcga ggagttcttc cggctgccgg cggaggacaa ggcggcgttc 300 tactccgacg cggaggagaa ccccaaccgc ctcttctcca gcaccatcta cgaggtcggc 360 gaccagcgct actggcgcga ctgcctccgc ctcgcctgcg gcttccccgt cgccgacgac 420 accaacaccc actggcccga caagccccac catctccggg atgtcacgga gaagttcttc 480 gtggcgacga ggggattggg gatcgagctg ctgcggctgc tgtgcgaggg gatggggctc 540 aggccggact acttcgagcg cgacctcacc gccggcgatg tcatcatcaa cgtcaaccac 600 taccctccat gcccggatcc gagcctgacg ctgggcttgc cgccgcactg cgaccgcaac 660 ctcatcaccc tgctcctcca gggcgacgtc ttcggcctcc aggtctccta caatggcgac 720 tggatcaacg tcgaccccgt ccccgacgcc ttcgtcgtca actttggcca cctcctcgag 780 attgcgacga acggagtgct gaagagcatc gagcacaggg cgatgacgaa ctcggcggtg 840 gcgaggacgt cggtggcgac gttcatgatg ccgccgatgg actgcctcgt cggaccggcg 900 aaggagctcg tcggagacgg cggccagccg cagtatcgca ccgtcacgtt ccgcgagttc 960 atgcgcatct acaagaccgt cggcgcgcgc cgcgacagcg tcgagaaggc cttcaaaatc 1020 tga 1023 50 340 PRT Oryza sativa 50 Met Glu Lys Leu Leu Ser Ser Ser Gly Ala Ala Ala Ala Val Ala Ser 1 5 10 15 Gln Gly Gln Leu Pro Asp Cys Phe Val Phe Pro Ala Asp Arg Arg Pro 20 25 30 Pro Ala Ser Thr Ala Ala Val Ser Leu Pro Val Ile Asp Leu Ser Gly 35 40 45 Pro Arg Asp Ala Val Arg Arg Ala Val Leu Asp Ala Gly Lys Glu Leu 50 55 60 Gly Phe Phe Gln Val Val Asn His Gly Val Pro Pro Glu Thr Met Arg 65 70 75 80 Glu Met Ala Ala Val Cys Glu Glu Phe Phe Arg Leu Pro Ala Glu Asp 85 90 95 Lys Ala Ala Phe Tyr Ser Asp Ala Glu Glu Asn Pro Asn Arg Leu Phe 100 105 110 Ser Ser Thr Ile Tyr Glu Val Gly Asp Gln Arg Tyr Trp Arg Asp Cys 115 120 125 Leu Arg Leu Ala Cys Gly Phe Pro Val Ala Asp Asp Thr Asn Thr His 130 135 140 Trp Pro Asp Lys Pro His His Leu Arg Asp Val Thr Glu Lys Phe Phe 145 150 155 160 Val Ala Thr Arg Gly Leu Gly Ile Glu Leu Leu Arg Leu Leu Cys Glu 165 170 175 Gly Met Gly Leu Arg Pro Asp Tyr Phe Glu Arg Asp Leu Thr Ala Gly 180 185 190 Asp Val Ile Ile Asn Val Asn His Tyr Pro Pro Cys Pro Asp Pro Ser 195 200 205 Leu Thr Leu Gly Leu Pro Pro His Cys Asp Arg Asn Leu Ile Thr Leu 210 215 220 Leu Leu Gln Gly Asp Val Phe Gly Leu Gln Val Ser Tyr Asn Gly Asp 225 230 235 240 Trp Ile Asn Val Asp Pro Val Pro Asp Ala Phe Val Val Asn Phe Gly 245 250 255 His Leu Leu Glu Ile Ala Thr Asn Gly Val Leu Lys Ser Ile Glu His 260 265 270 Arg Ala Met Thr Asn Ser Ala Val Ala Arg Thr Ser Val Ala Thr Phe 275 280 285 Met Met Pro Pro Met Asp Cys Leu Val Gly Pro Ala Lys Glu Leu Val 290 295 300 Gly Asp Gly Gly Gln Pro Gln Tyr Arg Thr Val Thr Phe Arg Glu Phe 305 310 315 320 Met Arg Ile Tyr Lys Thr Val Gly Ala Arg Arg Asp Ser Val Glu Lys 325 330 335 Ala Phe Lys Ile 340 51 2580 DNA Oryza sativa 51 atggcggcgg cgatggtggc ggcggtgcat ggagtgggga ggcaggacag gtcgtcgcct 60 ggcggcggag gggcgccgca agtggacacg ggcaagtacg tgcgctacac cccggagcag 120 gtggaggcgc tggagcgggt ctacggcgag tgccccaagc ccagctcgct ccgccgccag 180 cagctcatcc gcgagtgccc catactcagc aacatcgagc ccaagcagat caaggtctgg 240 ttccagaacc gcaggtgccg cgagaagcag cgcaaggagg catctcgcct gcaaactgtg 300 aaccggaagt tgactgcgat gaacaagctg ttgatggagg agaatgacag gctgcagaag 360 caggtgtccc gcctcgttta cgagaacggg tacatgcggc agcagctcca taatccttct 420 gtggcaacta cagacacgag ctgtgagtct gtggttacaa gtggtcaaca ccaccaacag 480 caaaacccag cagccacgcg tccgcaaagg gacgcgaaca acccagctgg tctactcgct 540 atagctgagg agaccttggc agagttcctg tcgaaagcga cgggtactgc tgtcgattgg 600 gtgcaaatgg ttgggatgaa gcctggtccg gattccattg gaatcatcgc tgtttcgcac 660 aattgtagtg gcgtagcagc acgagcttgc ggccttgtga gccttgagcc cacaaaggtt 720 gctgagatcc ttaaggatcg cccatcttgg tatcgcgatt gccggtgtgt ggatgtgctc 780 catgttatcc ctacgggtaa tggtggaact attgagctta tctacatgca gacttatgca 840 ccgacaactt tggcggcacc acgtgacttc tggatactcc gttacactag tggtcttgag 900 gatggaagtc ttgtgatctg tgagagatca ttgactcaat ccactggtgg cccatcagga 960 cctaacactc caaactttgt cagagccgag gtgcttccta gcggctattt gatccgccca 1020 tgtgaggggg gtggttccat gattcacatt gtggatcatg ttgatttgga tgcttggagt 1080 gtgcctgagg tccttagacc actttatgaa tctcctaaga tccttgcgca gaagatgaca 1140 attgctgcac tgcgtcacat taggcaaatt gcacatgaat caagtgggga aatgccctat 1200 ggagggggcc gtcagccagc agttctgaga acatttagtc agaggctaag cagaggcttc 1260 aatgatgctg tcaatggatt cccggatgat ggctggtcac tgatgagcag cgatggtgct 1320 gaggatgtga caattgcttt taactcatct ccaaacaagc ttgttggatc tcatgtcaac 1380 tcctcccagc tgttttctgc aattggaggc ggcatcttgt gtgcaaaggc atctatgctg 1440 ttacagaatg taccacctgc tctcctagtg cgatttttga gggagcaccg ctctgaatgg 1500 gctgatcctg gtgttgatgc ttattctgct gctgcgttga gggctagtcc atatgcagtt 1560 cctggtctgc gagctggtgg ttttatgggc agtcaggtta tattgccact tgcgcacacc 1620 ttagagcatg aagagttcct ggaggtcatt aggcttgagg gacacagcct ctgccatgat 1680 gaggtcgttc tatcaagaga tatgtacctt ctgcagctgt gcagcggtgt agatgaaaat 1740 gctgcgggtg catgtgccca gcttgtcttt gcacccattg acgaatcttt tgctgatgat 1800 gcaccactgc taccctcagg cttccgtgtg ataccactgg atggcaagac ggatgcacca 1860 tctgcgacac gcacacttga cctggcatct actcttgagg ttggatcggg tgggactaca 1920 cgggcttcta gtgacacctc gagcacctgc aacacaagat cggtcctgac catagctttc 1980 caattctcat atgaaaacca ccttcgtgaa agcgtagcgg caatggccag gcagtatgtc 2040 cggaccgtgg tggcatcagt gcagagagtg gccatggcaa tagctccttc acgtcttggt 2100 ggacagattg aaacaaagaa ccctccagga tctcctgagg cccatacgct tgcaaggtgg 2160 attgggagga gctaccgatt ccacactgga gcggatcccc ttcgcacaga ctcacaaagc 2220 acggattctt ccttgaaagc aatgtggcaa cactctgatt caatcatgtg ctgctccctg 2280 aaggctgctc ctgtgttcac cttcgccaac caagccggcc tcgacatgct ggagacgacg 2340 ctgattgctc tccaggacat ctcgctcgag aagatccttg atgatgatgg ccggaaggca 2400 ctatgtacag agttccccaa gatcatgcag cagggtttcg cctacctccc gggcggcgtg 2460 tgcgtgtcga gcatggggcg gccggtgtcg tacgagcagg cggtggcgtg gaaggtcctg 2520 agcgacgacg acacgccgca ctgcctcgcc ttcatgttcg tcaactggtc attcgtctga 2580 52 859 PRT Oryza sativa 52 Met Ala Ala Ala Met Val Ala Ala Val His Gly Val Gly Arg Gln Asp 1 5 10 15 Arg Ser Ser Pro Gly Gly Gly Gly Ala Pro Gln Val Asp Thr Gly Lys 20 25 30 Tyr Val Arg Tyr Thr Pro Glu Gln Val Glu Ala Leu Glu Arg Val Tyr 35 40 45 Gly Glu Cys Pro Lys Pro Ser Ser Leu Arg Arg Gln Gln Leu Ile Arg 50 55 60 Glu Cys Pro Ile Leu Ser Asn Ile Glu Pro Lys Gln Ile Lys Val Trp 65 70 75 80 Phe Gln Asn Arg Arg Cys Arg Glu Lys Gln Arg Lys Glu Ala Ser Arg 85 90 95 Leu Gln Thr Val Asn Arg Lys Leu Thr Ala Met Asn Lys Leu Leu Met 100 105 110 Glu Glu Asn Asp Arg Leu Gln Lys Gln Val Ser Arg Leu Val Tyr Glu 115 120 125 Asn Gly Tyr Met Arg Gln Gln Leu His Asn Pro Ser Val Ala Thr Thr 130 135 140 Asp Thr Ser Cys Glu Ser Val Val Thr Ser Gly Gln His His Gln Gln 145 150 155 160 Gln Asn Pro Ala Ala Thr Arg Pro Gln Arg Asp Ala Asn Asn Pro Ala 165 170 175 Gly Leu Leu Ala Ile Ala Glu Glu Thr Leu Ala Glu Phe Leu Ser Lys 180 185 190 Ala Thr Gly Thr Ala Val Asp Trp Val Gln Met Val Gly Met Lys Pro 195 200 205 Gly Pro Asp Ser Ile Gly Ile Ile Ala Val Ser His Asn Cys Ser Gly 210 215 220 Val Ala Ala Arg Ala Cys Gly Leu Val Ser Leu Glu Pro Thr Lys Val 225 230 235 240 Ala Glu Ile Leu Lys Asp Arg Pro Ser Trp Tyr Arg Asp Cys Arg Cys 245 250 255 Val Asp Val Leu His Val Ile Pro Thr Gly Asn Gly Gly Thr Ile Glu 260 265 270 Leu Ile Tyr Met Gln Thr Tyr Ala Pro Thr Thr Leu Ala Ala Pro Arg 275 280 285 Asp Phe Trp Ile Leu Arg Tyr Thr Ser Gly Leu Glu Asp Gly Ser Leu 290 295 300 Val Ile Cys Glu Arg Ser Leu Thr Gln Ser Thr Gly Gly Pro Ser Gly 305 310 315 320 Pro Asn Thr Pro Asn Phe Val Arg Ala Glu Val Leu Pro Ser Gly Tyr 325 330 335 Leu Ile Arg Pro Cys Glu Gly Gly Gly Ser Met Ile His Ile Val Asp 340 345 350 His Val Asp Leu Asp Ala Trp Ser Val Pro Glu Val Leu Arg Pro Leu 355 360 365 Tyr Glu Ser Pro Lys Ile Leu Ala Gln Lys Met Thr Ile Ala Ala Leu 370 375 380 Arg His Ile Arg Gln Ile Ala His Glu Ser Ser Gly Glu Met Pro Tyr 385 390 395 400 Gly Gly Gly Arg Gln Pro Ala Val Leu Arg Thr Phe Ser Gln Arg Leu 405 410 415 Ser Arg Gly Phe Asn Asp Ala Val Asn Gly Phe Pro Asp Asp Gly Trp 420 425 430 Ser Leu Met Ser Ser Asp Gly Ala Glu Asp Val Thr Ile Ala Phe Asn 435 440 445 Ser Ser Pro Asn Lys Leu Val Gly Ser His Val Asn Ser Ser Gln Leu 450 455 460 Phe Ser Ala Ile Gly Gly Gly Ile Leu Cys Ala Lys Ala Ser Met Leu 465 470 475 480 Leu Gln Asn Val Pro Pro Ala Leu Leu Val Arg Phe Leu Arg Glu His 485 490 495 Arg Ser Glu Trp Ala Asp Pro Gly Val Asp Ala Tyr Ser Ala Ala Ala 500 505 510 Leu Arg Ala Ser Pro Tyr Ala Val Pro Gly Leu Arg Ala Gly Gly Phe 515 520 525 Met Gly Ser Gln Val Ile Leu Pro Leu Ala His Thr Leu Glu His Glu 530 535 540 Glu Phe Leu Glu Val Ile Arg Leu Glu Gly His Ser Leu Cys His Asp 545 550 555 560 Glu Val Val Leu Ser Arg Asp Met Tyr Leu Leu Gln Leu Cys Ser Gly 565 570 575 Val Asp Glu Asn Ala Ala Gly Ala Cys Ala Gln Leu Val Phe Ala Pro 580 585 590 Ile Asp Glu Ser Phe Ala Asp Asp Ala Pro Leu Leu Pro Ser Gly Phe 595 600 605 Arg Val Ile Pro Leu Asp Gly Lys Thr Asp Ala Pro Ser Ala Thr Arg 610 615 620 Thr Leu Asp Leu Ala Ser Thr Leu Glu Val Gly Ser Gly Gly Thr Thr 625 630 635 640 Arg Ala Ser Ser Asp Thr Ser Ser Thr Cys Asn Thr Arg Ser Val Leu 645 650 655 Thr Ile Ala Phe Gln Phe Ser Tyr Glu Asn His Leu Arg Glu Ser Val 660 665 670 Ala Ala Met Ala Arg Gln Tyr Val Arg Thr Val Val Ala Ser Val Gln 675 680 685 Arg Val Ala Met Ala Ile Ala Pro Ser Arg Leu Gly Gly Gln Ile Glu 690 695 700 Thr Lys Asn Pro Pro Gly Ser Pro Glu Ala His Thr Leu Ala Arg Trp 705 710 715 720 Ile Gly Arg Ser Tyr Arg Phe His Thr Gly Ala Asp Pro Leu Arg Thr 725 730 735 Asp Ser Gln Ser Thr Asp Ser Ser Leu Lys Ala Met Trp Gln His Ser 740 745 750 Asp Ser Ile Met Cys Cys Ser Leu Lys Ala Ala Pro Val Phe Thr Phe 755 760 765 Ala Asn Gln Ala Gly Leu Asp Met Leu Glu Thr Thr Leu Ile Ala Leu 770 775 780 Gln Asp Ile Ser Leu Glu Lys Ile Leu Asp Asp Asp Gly Arg Lys Ala 785 790 795 800 Leu Cys Thr Glu Phe Pro Lys Ile Met Gln Gln Gly Phe Ala Tyr Leu 805 810 815 Pro Gly Gly Val Cys Val Ser Ser Met Gly Arg Pro Val Ser Tyr Glu 820 825 830 Gln Ala Val Ala Trp Lys Val Leu Ser Asp Asp Asp Thr Pro His Cys 835 840 845 Leu Ala Phe Met Phe Val Asn Trp Ser Phe Val 850 855 53 1113 DNA Oryza sativa 53 atgatgatgt cttcttcgca aacaccagta cggatcgcct tcgttttcct cgtcatcctc 60 gccgcgactg atgcgcacag cgaccaccga actccgccgc cggcgtgcgg aggcgcggcc 120 gtgggagggg aatgccacag cgtggccagg gcgctccgcc tgaagctgat cgccatcccg 180 gcgatcctcg ccgccagcgt ggccggcgtg tgcctgccga tcttcgcccg gtccgtgccg 240 gcgctccgcc ccgacggcgg cctcttcgcc gtcgtgaagg cgttcgcgtc gggcgtcatc 300 ctcggcaccg gctacatgca cgtgctcccg gactcgttca acgacctcac ctcgccgtgc 360 ctgcccagga agccatggcc ggagttcccg ttcgcggcgt tcgtcgccat gctcgccgcc 420 gtgttcacgc tcatggtgga ctcgctcatg ctcacgttcc acacgcgggg cagcaaggga 480 cgggccagca gcgccgtcgc gcaccacggc gaccacgggc actgtcacgc tcacgcgctg 540 gggcaagcag acgtcgctgc gctgtcgacg acggaggcgg cggatcaggg cagcggcgac 600 gtcgaggccg gtaacaccac caaggcgcag cttctcagga atcgcgtcat tgtgcaggtt 660 ctcgagatgg gcatcgtggt gcactcagtg gtgatcgggc tgggcatggg ggcgtcgcag 720 aacgtgtgca cgatccggcc gctggtggcg gcgctgtgct tccaccagat gttcgagggg 780 atggggctcg gcggctgcat cctgcaggcg gggtacggcg ggaggacgag gtcggcgctg 840 gtcttcttct tctccaccac gacgccgttc gggatcgcgc tggggctcgc gctgaccagg 900 gtgtacagcg acagcagccc gacggcgctg gtcgtcgtcg gcctgctcaa cgcggcgtcg 960 gcggggctgc tgcactacat ggcgctggtg gagctcctcg ccgccgattt catggggccc 1020 aagctgcagg gcaacgtccg tctccagctc gccgcgtccc tcgccatcct cctcggcgcc 1080 ggcggcatgt ccgtcatggc caagtgggcg tga 1113 54 370 PRT Oryza sativa 54 Met Met Met Ser Ser Ser Gln Thr Pro Val Arg Ile Ala Phe Val Phe 1 5 10 15 Leu Val Ile Leu Ala Ala Thr Asp Ala His Ser Asp His Arg Thr Pro 20 25 30 Pro Pro Ala Cys Gly Gly Ala Ala Val Gly Gly Glu Cys His Ser Val 35 40 45 Ala Arg Ala Leu Arg Leu Lys Leu Ile Ala Ile Pro Ala Ile Leu Ala 50 55 60 Ala Ser Val Ala Gly Val Cys Leu Pro Ile Phe Ala Arg Ser Val Pro 65 70 75 80 Ala Leu Arg Pro Asp Gly Gly Leu Phe Ala Val Val Lys Ala Phe Ala 85 90 95 Ser Gly Val Ile Leu Gly Thr Gly Tyr Met His Val Leu Pro Asp Ser 100 105 110 Phe Asn Asp Leu Thr Ser Pro Cys Leu Pro Arg Lys Pro Trp Pro Glu 115 120 125 Phe Pro Phe Ala Ala Phe Val Ala Met Leu Ala Ala Val Phe Thr Leu 130 135 140 Met Val Asp Ser Leu Met Leu Thr Phe His Thr Arg Gly Ser Lys Gly 145 150 155 160 Arg Ala Ser Ser Ala Val Ala His His Gly Asp His Gly His Cys His 165 170 175 Ala His Ala Leu Gly Gln Ala Asp Val Ala Ala Leu Ser Thr Thr Glu 180 185 190 Ala Ala Asp Gln Gly Ser Gly Asp Val Glu Ala Gly Asn Thr Thr Lys 195 200 205 Ala Gln Leu Leu Arg Asn Arg Val Ile Val Gln Val Leu Glu Met Gly 210 215 220 Ile Val Val His Ser Val Val Ile Gly Leu Gly Met Gly Ala Ser Gln 225 230 235 240 Asn Val Cys Thr Ile Arg Pro Leu Val Ala Ala Leu Cys Phe His Gln 245 250 255 Met Phe Glu Gly Met Gly Leu Gly Gly Cys Ile Leu Gln Ala Gly Tyr 260 265 270 Gly Gly Arg Thr Arg Ser Ala Leu Val Phe Phe Phe Ser Thr Thr Thr 275 280 285 Pro Phe Gly Ile Ala Leu Gly Leu Ala Leu Thr Arg Val Tyr Ser Asp 290 295 300 Ser Ser Pro Thr Ala Leu Val Val Val Gly Leu Leu Asn Ala Ala Ser 305 310 315 320 Ala Gly Leu Leu His Tyr Met Ala Leu Val Glu Leu Leu Ala Ala Asp 325 330 335 Phe Met Gly Pro Lys Leu Gln Gly Asn Val Arg Leu Gln Leu Ala Ala 340 345 350 Ser Leu Ala Ile Leu Leu Gly Ala Gly Gly Met Ser Val Met Ala Lys 355 360 365 Trp Ala 370 55 1200 DNA Oryza sativa 55 atggcggcgg gcggcggcgg agatggtggt ggtggtggtg ggcgggcggt gatcccgatg 60 ggacacggcg acccgtcggt gttcccgtgc ttccggacga cggcggacgc cgtggacgcc 120 gtggcggcgg cgctccggtc cggggagcac aactcctact cctcctgcgt cggcctcgag 180 cctgcacgga ggtctatcgc gcggtactta tcgcgagact tgccatatga gctatcagct 240 gatgatgtgt acctgacaag tggctgtgct caagcgattg agatcatctg ctctgtccta 300 gctcgccctg gtgccaacat cctgtgccca aggccagggt acctgttcca cgaggcacgc 360 gcagtgttca atggcatgga ggtcaggtac tttgatcttc tcccagagag tggctgggag 420 gttgatcttg atggagtgca ggaacttgct gacaagaaca cggttgcaat ggtcattatc 480 aatccaggaa atccctgtgg caatgtctac acttctgagc atttggccaa ggttgccgag 540 accgcgaaaa agcttggcat ctttgtcatt gcagatgaag tgtatgcaca tttgacgttt 600 gggcagaata aatttgtgcc gatgggggtg tttggctcag tagctccagt tcttacgtta 660 ggatcgatat cgaagagatg ggttgtgcct ggatggcgac ttggatggat tgtgacgagc 720 gatcctaatg gcgtatttca aaggaccaag gtagtggaaa gcatccagag ttaccttgat 780 atctcggctg atcctgcaac atttatccag ggagcaattc cacaactcat agagaacaca 840 aaggaagaat tcttcgaaaa gaccgtcgat gtcctaaggc agaccgcaga tatttgttgg 900 gagaagctga agggcatcag ttgcatcact tgcccaagca aacctgaggg ttccatgttt 960 gtcatggtga aactggatct gtcctgcctg caaggcatca aagatgacat ggacttctgc 1020 tgccagctag caaaggaaga attggtgatt cttttgccag gatgtgctgt tggatacaag 1080 aattggctcc gaatcacctt cgccatcgaa ccgtcttctc ttgaagatgg tattgatagg 1140 ctcaagtcct tctgctcgcg acatagcaag ccgaaagttc accggtctct tgaaacatga 1200 56 399 PRT Oryza sativa 56 Met Ala Ala Gly Gly Gly Gly Asp Gly Gly Gly Gly Gly Gly Arg Ala 1 5 10 15 Val Ile Pro Met Gly His Gly Asp Pro Ser Val Phe Pro Cys Phe Arg 20 25 30 Thr Thr Ala Asp Ala Val Asp Ala Val Ala Ala Ala Leu Arg Ser Gly 35 40 45 Glu His Asn Ser Tyr Ser Ser Cys Val Gly Leu Glu Pro Ala Arg Arg 50 55 60 Ser Ile Ala Arg Tyr Leu Ser Arg Asp Leu Pro Tyr Glu Leu Ser Ala 65 70 75 80 Asp Asp Val Tyr Leu Thr Ser Gly Cys Ala Gln Ala Ile Glu Ile Ile 85 90 95 Cys Ser Val Leu Ala Arg Pro Gly Ala Asn Ile Leu Cys Pro Arg Pro 100 105 110 Gly Tyr Leu Phe His Glu Ala Arg Ala Val Phe Asn Gly Met Glu Val 115 120 125 Arg Tyr Phe Asp Leu Leu Pro Glu Ser Gly Trp Glu Val Asp Leu Asp 130 135 140 Gly Val Gln Glu Leu Ala Asp Lys Asn Thr Val Ala Met Val Ile Ile 145 150 155 160 Asn Pro Gly Asn Pro Cys Gly Asn Val Tyr Thr Ser Glu His Leu Ala 165 170 175 Lys Val Ala Glu Thr Ala Lys Lys Leu Gly Ile Phe Val Ile Ala Asp 180 185 190 Glu Val Tyr Ala His Leu Thr Phe Gly Gln Asn Lys Phe Val Pro Met 195 200 205 Gly Val Phe Gly Ser Val Ala Pro Val Leu Thr Leu Gly Ser Ile Ser 210 215 220 Lys Arg Trp Val Val Pro Gly Trp Arg Leu Gly Trp Ile Val Thr Ser 225 230 235 240 Asp Pro Asn Gly Val Phe Gln Arg Thr Lys Val Val Glu Ser Ile Gln 245 250 255 Ser Tyr Leu Asp Ile Ser Ala Asp Pro Ala Thr Phe Ile Gln Gly Ala 260 265 270 Ile Pro Gln Leu Ile Glu Asn Thr Lys Glu Glu Phe Phe Glu Lys Thr 275 280 285 Val Asp Val Leu Arg Gln Thr Ala Asp Ile Cys Trp Glu Lys Leu Lys 290 295 300 Gly Ile Ser Cys Ile Thr Cys Pro Ser Lys Pro Glu Gly Ser Met Phe 305 310 315 320 Val Met Val Lys Leu Asp Leu Ser Cys Leu Gln Gly Ile Lys Asp Asp 325 330 335 Met Asp Phe Cys Cys Gln Leu Ala Lys Glu Glu Leu Val Ile Leu Leu 340 345 350 Pro Gly Cys Ala Val Gly Tyr Lys Asn Trp Leu Arg Ile Thr Phe Ala 355 360 365 Ile Glu Pro Ser Ser Leu Glu Asp Gly Ile Asp Arg Leu Lys Ser Phe 370 375 380 Cys Ser Arg His Ser Lys Pro Lys Val His Arg Ser Leu Glu Thr 385 390 395 57 999 DNA Oryza sativa 57 atggaggctc agaaccaaga ggtcgctgcc ctggtcgaga agatcgccgg cctccacgcc 60 gccatctcca agctgccgtc gctgagccca tccgccgagg tggacgcgct cttcaccgac 120 ctcgtcacgg cgtgcgtccc ggcgagcccc gtcgacgtgg ccaagctcgg cccggaggcg 180 caggcgatgc gggaggagct catccgcctc tgctccgccg ccgagggcca cctcgaggcg 240 cactacgccg acatgctcgc cgccttcgac aacccgctcg accacctcgc ccgcttcccg 300 tactacggca actacgtcaa cctgagcaag ctggagtacg acctcctcgt ccgctacgtc 360 cccggcattg cccccacccg cgtcgccttc gtcgggtcgg gcccgctgcc gttcagctcc 420 ctcgtgctcg ccgcgcacca cctgccggac gcggtgttcg acaactacga ccggtgcggc 480 gcggccaacg agcgggcgag gaggctgttc cgcggcgccg acgagggcct cggcgcgcgc 540 atggcgttcc acaccgccga cgtggcgacc ctgacggggg agctcggcgc gtacgacgtc 600 gtgttcctgg cggcgctcgt gggcatggcg gccgaggaga aggccggggt gatcgcgcac 660 ctgggcgcgc acatggcgga cggcgcggcg ctcgtcgtgc ggagcgcgca cggggcgcgc 720 gggttcctgt acccgatcgt cgatcccgag gacgtcaggc gtggcgggtt cgacgttctg 780 gcggtgtgcc acccggagga cgaggtgatc aactccgtca tcgtcgcccg caaggtcggt 840 gccgccgccg ccgccgccgc ggcgcgcaga gacgagctcg cggactcgcg cggcgtggtt 900 ctgccggtgg tcgggccgcc gtccacgtgc tgcaaggtgg aggcgagcgc ggttgagaag 960 gcagaagagt ttgccgccaa caaggagctg tccgtctaa 999 58 332 PRT Oryza sativa 58 Met Glu Ala Gln Asn Gln Glu Val Ala Ala Leu Val Glu Lys Ile Ala 1 5 10 15 Gly Leu His Ala Ala Ile Ser Lys Leu Pro Ser Leu Ser Pro Ser Ala 20 25 30 Glu Val Asp Ala Leu Phe Thr Asp Leu Val Thr Ala Cys Val Pro Ala 35 40 45 Ser Pro Val Asp Val Ala Lys Leu Gly Pro Glu Ala Gln Ala Met Arg 50 55 60 Glu Glu Leu Ile Arg Leu Cys Ser Ala Ala Glu Gly His Leu Glu Ala 65 70 75 80 His Tyr Ala Asp Met Leu Ala Ala Phe Asp Asn Pro Leu Asp His Leu 85 90 95 Ala Arg Phe Pro Tyr Tyr Gly Asn Tyr Val Asn Leu Ser Lys Leu Glu 100 105 110 Tyr Asp Leu Leu Val Arg Tyr Val Pro Gly Ile Ala Pro Thr Arg Val 115 120 125 Ala Phe Val Gly Ser Gly Pro Leu Pro Phe Ser Ser Leu Val Leu Ala 130 135 140 Ala His His Leu Pro Asp Ala Val Phe Asp Asn Tyr Asp Arg Cys Gly 145 150 155 160 Ala Ala Asn Glu Arg Ala Arg Arg Leu Phe Arg Gly Ala Asp Glu Gly 165 170 175 Leu Gly Ala Arg Met Ala Phe His Thr Ala Asp Val Ala Thr Leu Thr 180 185 190 Gly Glu Leu Gly Ala Tyr Asp Val Val Phe Leu Ala Ala Leu Val Gly 195 200 205 Met Ala Ala Glu Glu Lys Ala Gly Val Ile Ala His Leu Gly Ala His 210 215 220 Met Ala Asp Gly Ala Ala Leu Val Val Arg Ser Ala His Gly Ala Arg 225 230 235 240 Gly Phe Leu Tyr Pro Ile Val Asp Pro Glu Asp Val Arg Arg Gly Gly 245 250 255 Phe Asp Val Leu Ala Val Cys His Pro Glu Asp Glu Val Ile Asn Ser 260 265 270 Val Ile Val Ala Arg Lys Val Gly Ala Ala Ala Ala Ala Ala Ala Ala 275 280 285 Arg Arg Asp Glu Leu Ala Asp Ser Arg Gly Val Val Leu Pro Val Val 290 295 300 Gly Pro Pro Ser Thr Cys Cys Lys Val Glu Ala Ser Ala Val Glu Lys 305 310 315 320 Ala Glu Glu Phe Ala Ala Asn Lys Glu Leu Ser Val 325 330 59 1557 DNA Oryza sativa 59 atgggggtga cgaaggcgga ggcggttgcc ggcgacggcg ggaaggtggt ggacgacatc 60 gaggcgctcg ccgatctcag aaaggagcca gcatggaaaa ggtttttgtc ccacattgga 120 ccaggcttta tggtctgttt ggcttacctc gatcctggaa atatggagac tgatctacaa 180 gctggtgcca atcacaaata tgagcttctt tgggtgattt tgattggcct gatctttgca 240 ctgattatac aatcattatc ggctaatctt ggagtggtga cagggcgcca tcttgctgag 300 ctgtgcaaga ctgaatatcc agtatgggtg aaaacctgct tatggctgct agcagaacta 360 gctgtgattg cttccgatat tccagaagtt ataggtacag gatttgcttt caaccttttg 420 ttccacatac cagtgtggac cggggttctc attgctggct ctagcacgct tcttcttctt 480 ggactgcaaa gatatggggt aaggaaactg gaggttgtgg tcgcgctatt ggtgtttgtc 540 atggcagggt gcttcttcgt ggagatgagc atagtcaagc ctccggttaa tgaggtcctt 600 caaggattat tcatccccag gctcagtggg cccggtgcca caggagactc cattgccctt 660 cttggggctc ttgtaatgcc gcacaatcta ttcttgcact ctgccctggt gctgtcgagg 720 aatacacccg catcagcaaa aggaatgaag gatgtctgta ggttcttcct ctttgagagt 780 gggatagctc ttttcgtggc tctgcttgtc aacattgcaa tcatctctgt ctccggcact 840 gtatgtaatg caaccaacct ttcaccagaa gatgctgtaa aatgcagcga ccttacattg 900 gactcctcat ccttcctcct caggaatgtg ctaggaaagt caagtgcgac agtgtacggt 960 gtagcactct tggcttctgg acagagctcg accattactg gcacttatgc tgggcaatat 1020 gttatgcagg ggttcctaga catcaaaatg aaacagtggc ttcggaacct gatgacacgc 1080 agcattgcca ttgtgcctag cttaatcgtc tccatcattg gagggtctag tggcgccggt 1140 cgtctcatcg tcattgcatc gatgattcta tcctttgagc taccatttgc tctgatccct 1200 cttctcaagt tcagcagcag cagcaacaag atgggtgaaa acaagaactc catctatatt 1260 gttggattct cctgggtgct ggggttcgtc atcatcggga taaacatcta cttcctcagc 1320 acaaagctgg tcggctggat cctccacaac gcgctcccga cattcgccaa cgtgctcatc 1380 ggcatcgtgc tgttcccgct catgctgctc tacgtcgtcg ccgtgatcta cctgacgttc 1440 aggaaggaca ccgtcaagtt cgtgtctcgt cgtgagctgc aggccggcga cgacaccgag 1500 aaagcacagg tagccacctg cgtcgccgac gagcacagca aagagccacc cgtgtag 1557 60 518 PRT Oryza sativa 60 Met Gly Val Thr Lys Ala Glu Ala Val Ala Gly Asp Gly Gly Lys Val 1 5 10 15 Val Asp Asp Ile Glu Ala Leu Ala Asp Leu Arg Lys Glu Pro Ala Trp 20 25 30 Lys Arg Phe Leu Ser His Ile Gly Pro Gly Phe Met Val Cys Leu Ala 35 40 45 Tyr Leu Asp Pro Gly Asn Met Glu Thr Asp Leu Gln Ala Gly Ala Asn 50 55 60 His Lys Tyr Glu Leu Leu Trp Val Ile Leu Ile Gly Leu Ile Phe Ala 65 70 75 80 Leu Ile Ile Gln Ser Leu Ser Ala Asn Leu Gly Val Val Thr Gly Arg 85 90 95 His Leu Ala Glu Leu Cys Lys Thr Glu Tyr Pro Val Trp Val Lys Thr 100 105 110 Cys Leu Trp Leu Leu Ala Glu Leu Ala Val Ile Ala Ser Asp Ile Pro 115 120 125 Glu Val Ile Gly Thr Gly Phe Ala Phe Asn Leu Leu Phe His Ile Pro 130 135 140 Val Trp Thr Gly Val Leu Ile Ala Gly Ser Ser Thr Leu Leu Leu Leu 145 150 155 160 Gly Leu Gln Arg Tyr Gly Val Arg Lys Leu Glu Val Val Val Ala Leu 165 170 175 Leu Val Phe Val Met Ala Gly Cys Phe Phe Val Glu Met Ser Ile Val 180 185 190 Lys Pro Pro Val Asn Glu Val Leu Gln Gly Leu Phe Ile Pro Arg Leu 195 200 205 Ser Gly Pro Gly Ala Thr Gly Asp Ser Ile Ala Leu Leu Gly Ala Leu 210 215 220 Val Met Pro His Asn Leu Phe Leu His Ser Ala Leu Val Leu Ser Arg 225 230 235 240 Asn Thr Pro Ala Ser Ala Lys Gly Met Lys Asp Val Cys Arg Phe Phe 245 250 255 Leu Phe Glu Ser Gly Ile Ala Leu Phe Val Ala Leu Leu Val Asn Ile 260 265 270 Ala Ile Ile Ser Val Ser Gly Thr Val Cys Asn Ala Thr Asn Leu Ser 275 280 285 Pro Glu Asp Ala Val Lys Cys Ser Asp Leu Thr Leu Asp Ser Ser Ser 290 295 300 Phe Leu Leu Arg Asn Val Leu Gly Lys Ser Ser Ala Thr Val Tyr Gly 305 310 315 320 Val Ala Leu Leu Ala Ser Gly Gln Ser Ser Thr Ile Thr Gly Thr Tyr 325 330 335 Ala Gly Gln Tyr Val Met Gln Gly Phe Leu Asp Ile Lys Met Lys Gln 340 345 350 Trp Leu Arg Asn Leu Met Thr Arg Ser Ile Ala Ile Val Pro Ser Leu 355 360 365 Ile Val Ser Ile Ile Gly Gly Ser Ser Gly Ala Gly Arg Leu Ile Val 370 375 380 Ile Ala Ser Met Ile Leu Ser Phe Glu Leu Pro Phe Ala Leu Ile Pro 385 390 395 400 Leu Leu Lys Phe Ser Ser Ser Ser Asn Lys Met Gly Glu Asn Lys Asn 405 410 415 Ser Ile Tyr Ile Val Gly Phe Ser Trp Val Leu Gly Phe Val Ile Ile 420 425 430 Gly Ile Asn Ile Tyr Phe Leu Ser Thr Lys Leu Val Gly Trp Ile Leu 435 440 445 His Asn Ala Leu Pro Thr Phe Ala Asn Val Leu Ile Gly Ile Val Leu 450 455 460 Phe Pro Leu Met Leu Leu Tyr Val Val Ala Val Ile Tyr Leu Thr Phe 465 470 475 480 Arg Lys Asp Thr Val Lys Phe Val Ser Arg Arg Glu Leu Gln Ala Gly 485 490 495 Asp Asp Thr Glu Lys Ala Gln Val Ala Thr Cys Val Ala Asp Glu His 500 505 510 Ser Lys Glu Pro Pro Val 515 61 1395 DNA Oryza sativa 61 atgcgcccgg ccttctcgtg gcgcaagctg tggcggttca cggggcccgg gttcctcatg 60 tgcatcgcgt tcctcgaccc ggggaacctg gagggcgacc tgcaggccgg cgcggcggcg 120 gggtaccagc tgctgtggct gctgctgtgg gcgacggtca tgggcgccct ggtgcagctg 180 ctctccgcgc ggctcggggt cgccacgggg aagcacctcg ccgagctctg cagggaggag 240 tacccgccct gggccacgcg cgcgctctgg gccatgaccg agctcgcgct cgtcggcgcg 300 gacatccagg aggtgattgg cagcgcgatt gccatcaaga tcctctccgc tggcaccgtc 360 ccgctctggg gcggcgtcgt catcaccgcg ttcgattgct tcatcttttt attcctggag 420 aactatggag tgagaaaatt ggaagcattt ttcggagtcc tgattgcagt catggcagta 480 tcatttgcaa ttatgtttgg tgaaacaaag ccaagtggca aggagcttct gattggtttg 540 gtggttccaa agttgagttc aaggacaatc aaacaagcag ttggaattgt gggctgcata 600 atcatgcccc acaatgtctt cttgcactca gcactagtgc agtcaaggaa gattgacaca 660 aacaagaaat cccgtgttca agaagcagtg ttctattaca acattgagtc cattcttgcc 720 ctcattgtct cgttctttat taacatctgt gtcacaacag tttttgcgaa aggattttat 780 ggatctgaac aagctgatgg tataggtctt gagaatgctg gacagtactt acagcagaaa 840 tatgggactg cattctttcc tatactgtat atctgggcta ttgggctgtt agcatctgga 900 cagagtagca ctattactgg cacatatgca ggccaatttg ttatgggagg cttccttaat 960 cttcggttga agaagtggtt aagagcaatg attactcgaa gctttgcaat tattccaact 1020 atgattgtgg ctttattttt tgacacggag gatcctacaa tggacattct gaatgaggca 1080 ctcaatgttc ttcaatccat acagatacca tttgcactga ttcctctcat cacacttgtc 1140 tcaaaggagc aagtcatggg atcatttgtg gttggtccta tcacaaaagt gattagctgg 1200 attgttacag tattcttgat gctcatcaat gggtatctta tactgtcctt ctatgccact 1260 gaagtccggg gagcattggt tcggtcaagc ttgtgcgttg tattggcagt ttaccttgca 1320 ttcatcgtct atcttatcat gcgaaatacc tcactgtatt ctcgcctccg ctcagcaatg 1380 acaaagagca catga 1395 62 464 PRT Oryza sativa 62 Met Arg Pro Ala Phe Ser Trp Arg Lys Leu Trp Arg Phe Thr Gly Pro 1 5 10 15 Gly Phe Leu Met Cys Ile Ala Phe Leu Asp Pro Gly Asn Leu Glu Gly 20 25 30 Asp Leu Gln Ala Gly Ala Ala Ala Gly Tyr Gln Leu Leu Trp Leu Leu 35 40 45 Leu Trp Ala Thr Val Met Gly Ala Leu Val Gln Leu Leu Ser Ala Arg 50 55 60 Leu Gly Val Ala Thr Gly Lys His Leu Ala Glu Leu Cys Arg Glu Glu 65 70 75 80 Tyr Pro Pro Trp Ala Thr Arg Ala Leu Trp Ala Met Thr Glu Leu Ala 85 90 95 Leu Val Gly Ala Asp Ile Gln Glu Val Ile Gly Ser Ala Ile Ala Ile 100 105 110 Lys Ile Leu Ser Ala Gly Thr Val Pro Leu Trp Gly Gly Val Val Ile 115 120 125 Thr Ala Phe Asp Cys Phe Ile Phe Leu Phe Leu Glu Asn Tyr Gly Val 130 135 140 Arg Lys Leu Glu Ala Phe Phe Gly Val Leu Ile Ala Val Met Ala Val 145 150 155 160 Ser Phe Ala Ile Met Phe Gly Glu Thr Lys Pro Ser Gly Lys Glu Leu 165 170 175 Leu Ile Gly Leu Val Val Pro Lys Leu Ser Ser Arg Thr Ile Lys Gln 180 185 190 Ala Val Gly Ile Val Gly Cys Ile Ile Met Pro His Asn Val Phe Leu 195 200 205 His Ser Ala Leu Val Gln Ser Arg Lys Ile Asp Thr Asn Lys Lys Ser 210 215 220 Arg Val Gln Glu Ala Val Phe Tyr Tyr Asn Ile Glu Ser Ile Leu Ala 225 230 235 240 Leu Ile Val Ser Phe Phe Ile Asn Ile Cys Val Thr Thr Val Phe Ala 245 250 255 Lys Gly Phe Tyr Gly Ser Glu Gln Ala Asp Gly Ile Gly Leu Glu Asn 260 265 270 Ala Gly Gln Tyr Leu Gln Gln Lys Tyr Gly Thr Ala Phe Phe Pro Ile 275 280 285 Leu Tyr Ile Trp Ala Ile Gly Leu Leu Ala Ser Gly Gln Ser Ser Thr 290 295 300 Ile Thr Gly Thr Tyr Ala Gly Gln Phe Val Met Gly Gly Phe Leu Asn 305 310 315 320 Leu Arg Leu Lys Lys Trp Leu Arg Ala Met Ile Thr Arg Ser Phe Ala 325 330 335 Ile Ile Pro Thr Met Ile Val Ala Leu Phe Phe Asp Thr Glu Asp Pro 340 345 350 Thr Met Asp Ile Leu Asn Glu Ala Leu Asn Val Leu Gln Ser Ile Gln 355 360 365 Ile Pro Phe Ala Leu Ile Pro Leu Ile Thr Leu Val Ser Lys Glu Gln 370 375 380 Val Met Gly Ser Phe Val Val Gly Pro Ile Thr Lys Val Ile Ser Trp 385 390 395 400 Ile Val Thr Val Phe Leu Met Leu Ile Asn Gly Tyr Leu Ile Leu Ser 405 410 415 Phe Tyr Ala Thr Glu Val Arg Gly Ala Leu Val Arg Ser Ser Leu Cys 420 425 430 Val Val Leu Ala Val Tyr Leu Ala Phe Ile Val Tyr Leu Ile Met Arg 435 440 445 Asn Thr Ser Leu Tyr Ser Arg Leu Arg Ser Ala Met Thr Lys Ser Thr 450 455 460 63 1620 DNA Oryza sativa 63 atggcgcggc aggagcagca gcagcacctg caggtgctga gcgcgctgga cgcggcgaag 60 acgcagtggt accacttcac ggcgatcgtc gtcgccggca tgggcttctt caccgacgcc 120 tacgacctct tctgcatctc cctcgtcacc aagctgctcg gccgcatcta ctacaccgac 180 ctcgccaagg agaaccccgg cagcctgccg cccaacgtcg ccgcggcggt gaacggagtc 240 gcgttctgcg gcacgctggc ggggcagctc ttcttcgggt ggctcggcga caagctcggc 300 cggaagagcg tgtacgggat gacgctgctg atgatggtca tctgctccat cgcgtcgggg 360 ctctcgttct cgcacacgcc caccagcgtc atggcgacgc tctgcttctt ccggttctgg 420 ctcggattcg gcatcggcgg cgactacccg ctgtcggcga cgatcatgtc ggagtacgcc 480 aacaagaaga cccgcggcgc gttcatcgcc gccgtgttcg cgatgcaggg gttcggcatc 540 ctcgccggcg gcatcgtcac cctcatcatc tcctccgcgt tccgcgccgg gttcccggcg 600 ccggcgtacc aggacgaccg cgcgggctcc accgtccgcc aggccgacta cgtgtggcgg 660 atcatcctca tgctcggcgc catgccggcg ctgctcacct actactggcg gatgaagatg 720 ccggagacgg cgcgctacac cgccctcgtc gccaagaacg ccaagcaggc cgccgccgac 780 atgtccaagg tgctccaggt cgagatccag gaggagcagg acaagctgga gcagatggtg 840 acccggaaca gcagcagctt cggcctcttc tcccgccagt tcgcgcgccg ccacggcctc 900 cacctcgtcg gcaccgccac gacatggttc ctcctcgaca tcgccttcta cagccagaac 960 ctgttccaga aggacatctt caccagcatc aactggatcc ccaaggccaa gaccatgtcg 1020 gcgctggagg aggtgttccg catcgcgcgc gcccagacgc tcatcgccct gtgcggcacc 1080 gtcccgggct actggttcac cgtcttcctc atcgacatcg tcggccgctt cgccatccag 1140 ctgctagggt ttttcatgat gaccgtgttc atgctcggcc tcgccgtgcc gtaccaccac 1200 tggacgacga aggggaacca catcggcttc gtcgtcatgt acgccttcac cttcttcttc 1260 gccaacttcg gccccaactc caccaccttc atcgtgccgg cggagatctt cccggcgagg 1320 ctgcgttcca cctgccacgg catctcggcg gcggcgggga aggccggcgc catcatcgga 1380 tcgttcgggt tcctgtacgc ggcgcaggac ccgcacaagc ccgacgccgg gtacaaaccc 1440 gggatcgggg tgaggaactc gctgttcgtg ctcgccggat gcaacctgct cgggttcatc 1500 tgcacgttcc tcgtgccgga gtcgaagggg aagtcgctgg aggagatgtc cggcgaggcg 1560 gaggacgacg acgacgaggt ggccgccgcc ggcggtggcg ccgccgtgcg gccgctctag 1620 64 539 PRT Oryza sativa 64 Met Ala Arg Gln Glu Gln Gln Gln His Leu Gln Val Leu Ser Ala Leu 1 5 10 15 Asp Ala Ala Lys Thr Gln Trp Tyr His Phe Thr Ala Ile Val Val Ala 20 25 30 Gly Met Gly Phe Phe Thr Asp Ala Tyr Asp Leu Phe Cys Ile Ser Leu 35 40 45 Val Thr Lys Leu Leu Gly Arg Ile Tyr Tyr Thr Asp Leu Ala Lys Glu 50 55 60 Asn Pro Gly Ser Leu Pro Pro Asn Val Ala Ala Ala Val Asn Gly Val 65 70 75 80 Ala Phe Cys Gly Thr Leu Ala Gly Gln Leu Phe Phe Gly Trp Leu Gly 85 90 95 Asp Lys Leu Gly Arg Lys Ser Val Tyr Gly Met Thr Leu Leu Met Met 100 105 110 Val Ile Cys Ser Ile Ala Ser Gly Leu Ser Phe Ser His Thr Pro Thr 115 120 125 Ser Val Met Ala Thr Leu Cys Phe Phe Arg Phe Trp Leu Gly Phe Gly 130 135 140 Ile Gly Gly Asp Tyr Pro Leu Ser Ala Thr Ile Met Ser Glu Tyr Ala 145 150 155 160 Asn Lys Lys Thr Arg Gly Ala Phe Ile Ala Ala Val Phe Ala Met Gln 165 170 175 Gly Phe Gly Ile Leu Ala Gly Gly Ile Val Thr Leu Ile Ile Ser Ser 180 185 190 Ala Phe Arg Ala Gly Phe Pro Ala Pro Ala Tyr Gln Asp Asp Arg Ala 195 200 205 Gly Ser Thr Val Arg Gln Ala Asp Tyr Val Trp Arg Ile Ile Leu Met 210 215 220 Leu Gly Ala Met Pro Ala Leu Leu Thr Tyr Tyr Trp Arg Met Lys Met 225 230 235 240 Pro Glu Thr Ala Arg Tyr Thr Ala Leu Val Ala Lys Asn Ala Lys Gln 245 250 255 Ala Ala Ala Asp Met Ser Lys Val Leu Gln Val Glu Ile Gln Glu Glu 260 265 270 Gln Asp Lys Leu Glu Gln Met Val Thr Arg Asn Ser Ser Ser Phe Gly 275 280 285 Leu Phe Ser Arg Gln Phe Ala Arg Arg His Gly Leu His Leu Val Gly 290 295 300 Thr Ala Thr Thr Trp Phe Leu Leu Asp Ile Ala Phe Tyr Ser Gln Asn 305 310 315 320 Leu Phe Gln Lys Asp Ile Phe Thr Ser Ile Asn Trp Ile Pro Lys Ala 325 330 335 Lys Thr Met Ser Ala Leu Glu Glu Val Phe Arg Ile Ala Arg Ala Gln 340 345 350 Thr Leu Ile Ala Leu Cys Gly Thr Val Pro Gly Tyr Trp Phe Thr Val 355 360 365 Phe Leu Ile Asp Ile Val Gly Arg Phe Ala Ile Gln Leu Leu Gly Phe 370 375 380 Phe Met Met Thr Val Phe Met Leu Gly Leu Ala Val Pro Tyr His His 385 390 395 400 Trp Thr Thr Lys Gly Asn His Ile Gly Phe Val Val Met Tyr Ala Phe 405 410 415 Thr Phe Phe Phe Ala Asn Phe Gly Pro Asn Ser Thr Thr Phe Ile Val 420 425 430 Pro Ala Glu Ile Phe Pro Ala Arg Leu Arg Ser Thr Cys His Gly Ile 435 440 445 Ser Ala Ala Ala Gly Lys Ala Gly Ala Ile Ile Gly Ser Phe Gly Phe 450 455 460 Leu Tyr Ala Ala Gln Asp Pro His Lys Pro Asp Ala Gly Tyr Lys Pro 465 470 475 480 Gly Ile Gly Val Arg Asn Ser Leu Phe Val Leu Ala Gly Cys Asn Leu 485 490 495 Leu Gly Phe Ile Cys Thr Phe Leu Val Pro Glu Ser Lys Gly Lys Ser 500 505 510 Leu Glu Glu Met Ser Gly Glu Ala Glu Asp Asp Asp Asp Glu Val Ala 515 520 525 Ala Ala Gly Gly Gly Ala Ala Val Arg Pro Leu 530 535 

What is claimed is:
 1. An isolated nucleic acid molecule comprising or consisting of a nucleotide sequence, its complement, or its reverse complement, encoding a polypeptide including: a) a polypeptide sequence listed in even numbered sequences of SEQ ID Nos:2-64, or a fragment, domain, repeat, feature, or chimera thereof; b) a polypeptide sequence having substantial similarity to (a); c) a polypeptide sequence encoded by a nucleotide sequence identical to or having substantial similarity to a nucleotide sequence listed in odd numbered sequences of SEQ ID Nos:1-63, or a fragment, domain, or feature thereof, or a sequence complementary thereto; d) a polypeptide sequence encoded by a nucleotide sequence capable of hybridizing under medium stringency conditions to a nucleotide sequence listed in odd numbered sequences of SEQ ID Nos:1-63, or to a sequence complementary thereto; and e) a functional fragment of (a), (b), (c) or (d).2. An isolated nucleic acid of claim 1, comprising a nucleotide sequence including: a) a nucleotide sequence listed in odd numbered sequences of SEQ ID NO:1-63, fragment, domain, or feature thereof; b) a nucleotide sequence having substantial similarity to (a); c) a nucleotide sequence capable of hybridizing to (a); d) a nucleotide sequence complementary to (a), (b) or (c); and e) a nucleotide sequence which is the reverse complement of (a), (b) or (c).
 3. An expression cassette comprising a promoter and the nucleic acid molecule of claim
 1. 4. A recombinant vector comprising the expression cassette of claim
 3. 5. A cell comprising the expression cassette of claim
 3. 6. A transgenic plant comprising the expression cassette of claim
 3. 7. Progeny and seed from the transgenic plant of claim
 6. 8. The transgenic plant of claim 6, wherein the expression cassette is expressed in the tissue of the epidermis, root, vascular tissue, meristem, cambium, cortex, pith, leaf, and flower.
 9. The plant of claim 6, wherein the plant has altered abiotic stress tolerance, enhanced yield, altered disease resistance, or altered nutritional content.
 10. The transgenic plant of claim 6, wherein the plant is selected from the group consisting of: rice, wheat, barley, rye, corn, potato, canola, soybean, sunflower, carrot, sweet potato, sugarbeet, bean, pea, chicory, lettuce, cabbage, cauliflower, broccoli, turnip, radish, spinach, asparagus, onion, garlic, eggplant, pepper, celery, squash, pumpkin, cucumber, apple, pear, quince, melon, plum, cherry, peach, nectarine, apricot, strawberry, grape, raspberry, blackberry, pineapple, avocado, papaya, mango, banana, soybean, tobacco, tomato, sorghum and sugarcane.
 11. The transgenic plant of claim 10, wherein the plant is rice.
 12. The transgenic plant of claim 6, wherein the plant is a monocot.
 13. The transgenic plant of claim 12, wherein the monocot is selected from the group consisting ofL maize, wheat, barley, oats, rye, millet, sorghum, trticale, secale, einkorn, spelt, emmer, teff, milo, flax, gramma grass, Tripsacum, and teosinte.
 14. A transgenic plant comprising the nucleic acid molecule of claim
 2. 15. Progeny and seed from the transgenic plant of claim
 14. 16. A method of altering the abiotic stress tolerance of a plant, comprising expressing an expression cassette comprising a nucleic acid molecule encoding a polypeptide having SEQ ID NO:2, 4, 6, 8, or 10 in a plant.
 17. A method of altering pathogen or disease resistance in a plant, comprising expressing an expression cassette comprising a nucleic acid molecule encoding a polypeptide having SEQ ID NO:12, 14, 16, 18, 20, 22, or 24 in the plant.
 18. A method of altering the grain quality, nutritional composition or yield of a plant, comprising expressing an expression cassette comprising a nucleic acid molecule encoding a polypeptide having SEQ ID NO:26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62 or
 64. 19. The method of claim 18, wherein the altered grairi quality, nutritional composition or yield is altered starch level, altered thiamin level, altered lysine level, altered iron level, altered aleurone enzyme levels, altered vitamin E content, altered protein level, altered time to harvest, altered seed number, altered iron acquisition, or altered phosphate acquisition.
 20. A shuffled nucleic acid containing a plurality of nucleotide sequence fragments, wherein at least one of the fragments corresponds to a region of a nucleotide sequence listed in odd numbered sequences of SEQ ID NOS:1-63, and wherein at least two of the plurality of sequence fragments are in an order, from 5′ to 3′ which is not an order in which the plurality of fragments naturally occur in a nucleic acid.
 21. A polypeptide comprising: a) a polypeptide sequence of SEQ ID NO:2; b) a polypeptide sequence having substantial similarity to (a); c) a polypeptide sequence encoded by a nucleotide sequence identical or substantially similar to a nucleotide sequence of SEQ ID NO:1; d) a polypeptide sequence encoded by a nucleic acid molecule capable of hybridizing under high stringency conditions to a nucleic acid molecule listed in SEQ ID NO:1 or to a sequence complementary thereto; and e) a functional fragment of (a), (b), (c) or (d).
 22. A method of producing a polypeptide of claim 21, comprising the steps of: a) growing recombinant cells comprising an expression cassette under suitable growth conditions, the expression cassette comprising a nucleic acid molecule of claim 1; and b) isolating the polypeptide from the recombinant cells.
 23. A method of decreasing the expression of a nucleic acid molecule of claim 1 in a plant comprising: (a) expressing in said plant a DNA molecule of claim 1 or a portion thereof in “sense” orientation; or (b) expressing in said plant a DNA molecule of claim 1 or a portion thereof in “anti-sense” orientation; or (c) expressing in said plant a ribozyme capable of specifically cleaving a messenger RNA transcript encoded by an endogenous gene corresponding to a DNA molecule of claim 1; or (d) expressing in a plant an aptamer specifically directed to a protein encoded by a DNA molecules of claim 1; or (e) expressing in a plant a mutated or a truncated form of a DNA molecule of claim 1; (f) modifying by homologous recombination in a plant at least one chromosomal copy of the gene corresponding to a DNA molecule of claim 1; or g) modifying by homologous recombination in a plant at least one chromosomal copy of the regulatory elements of a gene corresponding to any one of the DNA molecules of claim 1; or h) expressing in said plant a DNA molecule of claim 1 or a portion thereof in the “sense” and “antisense” orientation.
 28. An antibody cross-reactive to the polypeptide of claim
 21. 29. The polypeptide of claim 21, wherein the polypeptide is involved in a function such as abiotic stress tolerance, enhanced yield, disease resistance or nutritional content.
 30. A method of altering the expression of a polypeptide of claim 21 in a plant, comprising the step of expressing an expression cassette of claim 3 in the plant.
 31. The method of claim 30, wherein the polypeptide is expressed in a specific location or tissue of a plant.
 32. The method of claim 31, wherein the location or tissue is the epidermis, root, vascular tissue, meristem, cambium, cortex, pith, leaf, flower or seed.
 33. An isolated product from the plant which comprises an expression cassette comprising a promoter sequence operably linked to an isolated nucleic acid comprising a nucleotide sequence including: a) a nucleotide sequence listed in odd numbered sequences of SEQ ID NOS:1-63, or fragment, domain, or feature thereof; b) a nucleotide sequence encoding a polypeptide listed in even numbered sequences of SEQ ID NOS: 2-64; c) a nucleotide sequence having substantial similarity to (a) or (b); d) a nucleotide sequence capable of hybridizing to (a) or (b); e) a nucleotide sequence complementary to (a), (b), (c) or (d); and f) a nucleotide sequence that is the reverse complement of (a), (b), (c) or (d) according to the present disclosure.
 34. The isolated product of claim 33, wherein the isolated product includes an enzyme, a nutritional protein, a structural protein, an amino acid, a lipid, a fatty acid, a polysaccharide, a sugar, an alcohol, an alkaloid, a carotenoid, a propanoid, a steroid, a pigment, a vitamin or a plant hormone.
 35. A method of producing a recombinant protein, comprising the steps of: (a) growing recombinant cells comprising a nucleic acid construct under suitable growth conditions, the construct comprising an expression vector and a nucleic acid including: a nucleic acid encoding a protein as listed in even numbered nucleotide sequences of SEQ ID NOS:2-64, or a nucleic acid sequence listed in odd numbered nucleotide sequences of SEQ ID NOS:1-63, or segments thereof; and (b) isolating from the recombinant cells the recombinant protein expressed thereby.
 36. The method of claim 35, wherein the expression vector includes one or more elements of a promoter-enhancer sequence, a selection marker sequence, an origin of replication, an epitope-tag encoding sequence, an affinity purification-tag encoding sequence, a polyamino acid binding substance, or chitin-binding domain. 